His coaching career begun in 1997–98 for Serie D team Milazzo, where he nearly won the league at his debut, ending in second place. However, his outbreak came at Paternò, which he led on two consecutive promotions from Serie D to Serie C1. He then signed for Serie C2 Foggia, which he led to an immediate Serie C1 promotion. He made his Serie B debut in 2004–05 with Arezzo, replacing Mario Somma. Fired in the half-season and replaced by Marco Tardelli, he was successively recalled at the helm of the team, ending in 14th place.
In 2005 he became coach of Catania: in his first season for the rossoblu, Marino brought the team back to Serie A after over 20 years. He also coached Catania in its 2006–07 Serie A campaign. After a very impressive start that brought Catania up to the highest table positions, Catania experienced a negative streak following the riots in the Sicilian derby which caused the death of a policeman and resulted in the Catania home stadium to be disqualified for the remainder of the season. After Catania saved in the last matchday, thanks to a 2–1 win to relegation rivals Chievo, Marino announced he was going to leave his post. He later signed a four-year contract with Udinese. Speaking to SkyItalia in the post-match interview, Marino didn't hide his disappointment following the lacklustre display by his side against bottom placed Reggina. “We were awful this afternoon, and despite having a numerical advantage, it seemed as if we were the team playing in nine men," snarled Marino. "I am very disappointed with the display, despite the positive result. I certainly was not expecting such a poor display from my men today, as I expect everyone to give their all when they put on the Zebrette shirt.”
He was stripped of his managerial duties on December 22, 2009, as Udinese failed to impress in the first half of the 2009–10 season, and was replaced by Gianni De Biasi. He was appointed back at the helm of Udinese on February 21, 2010, after De Biasi was sacked due to poor results.
On June 2010 he was appointed new head coach of Parma, replacing Francesco Guidolin. On April 3, 2011 Marino, after the home defeat with Bari was sacked. On 22 December 2011, he was appointed the new head coach of Genoa to replace Alberto Malesani who was sacked after a disastrous 1–6 away defeat against Napoli. Marino's tenure as Genoa coach however turned out to be rather disappointing, as he did not manage to bring the team back into the fight for a European competition spot and instead left it close to the relegation zone; he was ultimately dismissed on 2 April 2012 after a 4–5 loss to Inter, and replaced by his predecessor Alberto Malesani.
He then accepted an offer to become new head coach of Serie B promotion hopefuls Pescara for the 2013–14 season, but was dismissed later throughout the season due to poor results.