This friction has been due to disputes including the self annexation of the Hatay Province to Turkey in 1939, water disputes resulting from the Southeastern Anatolia Project, and Syria's support for the Kurdistan Worker's Party (abbreviated as PKK) and the now-dissolved Armenian Secret Army for the Liberation of Armenia (abbreviated as ASALA) which has been recognised as a terrorist organisation by NATO, EU, and many other countries. Relations improved greatly after October 1998, when PKK leader Abdullah Öcalan was expelled by Syrian authorities. However, the Syrian civil war has once again strained relations between the two countries, leading to the suspension of diplomatic contact. A serious incident occurred with the Syrian downing of a Turkish military training flight in June 2012, resulting in Turkey calling an emergency meeting of NATO.
Syria normally maintains an embassy in Ankara and two consulates–general in Istanbul and Gaziantep. Turkey has an embassy in Damascus and a consulate–general in Aleppo. Diplomatic relations has been severed due to the Syrian civil war. Both countries are full members of the Union for the Mediterranean and the Organisation of Islamic Cooperation (OIC).
In 1938, the Sanjak of Alexandretta became independent from the French mandate of Syria as the Republic of Hatay, and following a referendum, 8 months later in 1939, it decided to join Turkey as the Hatay Province. This self-annexation was never recognized by Syria, which continues to show the Hatay Province of Turkey as part of Syria's territory on maps.
At present, Syrians hold the view that this land is historically Syrian and was illegally ceded in the late 1930s to Turkey by France – the mandatory occupying power of Syria (between 1920 and 1946). The Turks remember Syria as a former Ottoman vilayet. In 1938, the Turkish Army went into the former Syrian Mediterranean province with French approval and expelled most of its Alawite Arab and Armenian inhabitants. Before this, Alawi Arabs and Armenians were the majority of the provincial population. For the referendum, Turkey crossed tens of thousands of Turks into Alexandretta to vote.
In 1938, the province declared its independence from France and the following 29 June, the parliament of the newly declared Hatay Republic voted to join Turkey. This referendum has been labeled both "phoney" and "rigged", and that it was a way for the French to let Turks take over the area, hoping that they would turn on Hitler. The Syrian government recognized this decision in 2004 and gave up on territorial claims. Syrians still consider this land as integral Syrian territory. Syrians call this land Liwaaa aliskenderuna rather than the Turkish name of Hatay.
Water disputes have been a major source of conflict as Turkey has constructed several dams on the Euphrates and Tigris rivers as part of the Southeastern Anatolia Project- GAP to develop the region. The project GAP was aimed at reducing the harsh living conditions of the Southeastern provinces of Turkey by building 19 dams on the rivers of Euphrates and Tigris. This project, however, would seriously reduce Syrian water resources.
In addition to this, Euphrates and Tigris are not the only rivers that tangles Turkish-Syrian relations, the water distribution of Orantes River which pours into Mediterranean from the province of disputed Hatay also rises problems between two states.
Support to the PKK
Turkey has condemned Syria for supporting the PKK, which is listed as a terrorist organization internationally by a number of states and organizations, including the USA, NATO, and the EU and has claimed that Syria employed Alois Brunner to train Kurdish militants for attacks against Turkey.
The two countries came to the brink of war when Turkey threatened military action if Syria continued to shelter Abdullah Öcalan in Damascus, his long-time safe haven. Relations have improved since October 1998, when Öcalan was expelled by Damascus and Syria pledged to stop harbouring the PKK militants and the 1999 signing of the Adana agreement, following his subsequent capture in Kenya, envisaged security cooperation between the two countries.
In The New Turkey (Granta Books, 2005) BBC correspondent Chris Morris claims that Syria was "for years a bitter foe" as "Turkey's secular democracy, its application for EU membership and its close relationship with the United States have long been regarded in Tehran, Baghdad and Damascus with intense suspicion. Islamists look at the secular state which buried the caliphate and think 'betrayal'; and Arab nationalists still haven't forgotten that Turks are their former colonial rulers." "But there's been a thaw, especially since the AKP came to power," and "the new Turkish model – trying to mix greater democracy and Islam together – is now the subject of curiosity and not a little envy."
The Turkish Parliament's refusal to cooperate militarily with the 2003 invasion of Iraq was a turning point in Syrian-Turkish bilateral relations as Syria's perceptions of Turkey as incapable of acting independently were altered.
In late 2004, Turkish Prime Minister Recep Tayyip Erdoğan flew to Damascus to sign a free trade agreement in the follow-up to former Turkish President Turgut Özal's high-level trade negations with Syrian authorities, which included the first ever visit to Turkey by a Syrian President, in the 1990s and Erdoğan's own recently successful bid to initiate a Turkish EU accession which would allow Europe, "to extend its reach to the borders Syria, Iraq and Iran."
In 2008, Turkey was, as a sign of mutual trust in Damascus and Tel Aviv, invited to play the role of facilitator between Syria and Israel to solve their dispute over control over the Golan Heights, but these talks were abandoned after four rounds, following the deterioration in Turkey-Israel relations after Turkish Prime Minister Erdoğan criticised Israel's conduct of the 2008–2009 Israel-Gaza conflict as a "crime against humanity."
On 26 April 2009, the two states announced an "unprecedented" three-day military manoeuvre involving ground forces along their mutual border in what was described as "a step farther in their ever expanding cooperation." According to Turkish military sources, "The aim of the exercise is to boost friendship, cooperation, and confidence between the two countries land forces, and to increase the ability of border troops to train and work together." The exercise which commenced on 27 April involved teams from each country crossing the border to visit outposts.
Visiting Syrian Defense Minister Hasan Turkmani and Turkish Defense Minister Vecdi Gönül also signed a letter of intent giving the green light for cooperation in the defence industry, on the sidelines of the 9th International Defence Industry Fair (IDEF'09) that commenced in Istanbul the same day, as a sign of the level of political relations reached between the two states, although a Turkish defence industry source emphasised that, "it does not mean that the two countries will immediately enter into cooperation in arms production."
2009 Turkish Presidential visit to Syria
Turkish President Gül's 15–17 May official visit to Syria was made at the invitation of Damascus in reciprocation of Syrian President Assad's 2007 official visit to Turkey. A senior Turkish diplomat confirmed that, "The main topic on the agenda and the goal of the visit is the maintenance of momentum that has built up in bilateral relations within the last decade." The Turkish delegation included Foreign Minister Ahmet Davutoğlu, Foreign Trade Minister Zafer Çağlayan, Agriculture Minister and Culture and Tourism Minister Ertuğrul Günay.
Shortly before the visit new Syrian Ambassador to Turkey, Nidal Qablan confirmed that Syria was ready to restart the Turkish mediated peace negotiations with Israel and Gül supported the call, following his meeting with Assad, stating that, "We have heard Syria say it is ready to resume the peace talks from the point where they stopped with the previous [Israeli] government. We in Turkey are also ready." Assad confirmed, "Turkey's role is important because we have trust in Turkey." Israeli President Shimon Peres dismissed these calls stating, "The Syrians should be ready to talk. If President al-Assad wants peace, why is he shy? We suggested direct talks many times. He thinks direct talks are a prize for Israel. It's not a prize. It's normal."
Friction due to Syrian civil war
Since the Syrian Civil War, Diplomatic ties between Syria and Turkey greatly deteriorated. The Syrian civil war began to impact Turkey when at least 3,000 Syrian refugees fled crackdowns by the Syrian Army on towns such as Jisr ash-Shugur. In June, Turkish Prime Minister Erdogan described to Anatolian Agency his feeling that "They [Syria] are not acting in a humane manner. This is savagery." Earlier in May, he advised the Syrian government to not initiate another Hama massacre. However, the Turkish government is currently refraining from describing the Syrians who have fled as "refugees" or "asylum-seekers", instead referring to them as guests, and Erdogan, while demanding for implementation of promised reforms by the Syrian government, is currently refraining from calling for Bashar al-Assad's departure.
On 9 August 2011, BBC and numerous other news sites reported that Turkey is sending its foreign minister, Ahmet Davutoğlu, to Syria to give the government a "tough" message. Erdogan has said that he is becoming impatient with the "savagery" of Bashar al-Assad's government. Ahmet Davutoğlu also announced that "We are completely suspending all of these trade relations, all agreements between Turkey and Syria have been suspended."
The Turkish pilgrim bus attack occurred on November 21, 2011 when two buses carrying Turkish pilgrims returning from Saudi Arabia came under fire from Syrian soldiers. The attack occurred at a checkpoint near Homs, as a convoy of eight or nine Turkish buses was making its way towards Turkey via the Bab Hawa border crossing. The gunfire left two people injured. According to a driver, when told that the passengers were Turks, "Syrian soldiers emerged from behind sandbags and cursed Recep Tayyip Erdogan... Then they suddenly opened fire at the bus."
On 22 June 2012, Syria shot down a Turkish Air Force RF-4E reconnaissance jet near the Turkish-Syrian border. The Syrian military alleges the jet had violated Syrian airspace. However, Turkish president Abdullah Gül and other spokesmen have not confirmed this and emphasized that brief incursions into neighboring airspace by high-speed jets are routine occurrences. Gül stated that "it is not possible to cover over a thing like this. Whatever is necessary will no doubt be done." The Turkish and Syrian navies conducted a search for Turkish airmen downed by the incident.
In August 2012, Turkey began to hold high level meetings with the USA on plans to replace the Syrian government.
On 3 October 2012, Turkey attacked troops in Syria, after a Syrian mortar shell killed five people. Turkish parliament approved cross border operations. Turkish Prime Minister Tayyip Erdogan announced October 5 "We are not interested in war, but we're not far from it either,"
On 10 October 2012, Turkish Air Force F-16s intercepted a Syrian Air Airbus A320, flight RB442 from Moscow to Damascus, in Turkish airspace and forced it to land at Esenboğa International Airport, suspecting it was carrying Russian-made weapons. Inspectors confiscated military communications equipment and items "thought to be missile parts". Syria accused Turkey of "air piracy". On the same day the airline chief said in an interview that Turkey violated the Convention on International Civil Aviation Syria subsequently banned Turkish civilian flights from its airspace.
On 11 May 2013, Turkish security forces found a 2 kg cylinder with sarin gas after searching the homes of Syrian militants from the Al-Qaeda linked Al-Nusra Front who were previously detained, Turkish media reports. The gas was reportedly going to be used in a bomb. Russia asked Turkey for information about this. Where did the sarin gas come from? Why does Turkey produce so much Sarin Gas?,
On 11 May 2013, two car bombs exploded in the town of Reyhanlı, Hatay Province, Turkey. At least 43 people were killed and 140 more were injured in the attack. The car bombs were left outside Reyhanlı's town hall and post office. The first exploded at around 13:45 local time (10:45 GMT) and the second exploded about 15 minutes later. People attempting to help those injured in the first explosion were caught in the second blast. This attack was the deadliest single act of terrorism to occur on Turkish soil.
On 23 March 2014, Turkey shot down a Syrian combat jet Turkish-Syrian border. Initial announcement was made by Turkish prime minister Recep Tayyip Erdogan in a speech during Turkish local elections, 2014 campaign. Turkey claims that two Turkish Air Force F-16s downed the plane that was heading Turkish territory and ignored warnings, as a result of the infringement of the new engagement rules declared by the Republic of Turkey, after Syria shooting down a Turkish reconnaissance plane in 22 June 2012.  The pilot jumped off the plane according the witness reports. Syria condemned the aggression and argues that the plane was following rebels and it did not violate Turkish airspace. However, according to the new engagement rules, two countries could defend themselves if the other come close to their borders, perceiving the action as a threat. 
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