Early career 
Sebastian was born in Extremadura, Spain. He saw military service in the Spanish invasion of Portugal during 1580–1583. He was going to New Spain in 1583, he sailed as a merchant on the Manila galleon to the Philippines in 1586–1589. In 1587 he was on board the Santa Ana when it was captured by Thomas Cavendish.
The Californias 
In 1593 the disputed concession for pearl fishing on the western shores of the Gulf of California was transferred to Vizcaíno. He succeeded in sailing with three ships to La Paz, Baja California Sur in 1596. He gave this site (known to Hernándo Cortés as Santa Cruz) its modern name and attempted to establish a settlement. However, problems of resupply, declining morale, and a fire soon forced its abandonment. He also became a diplomat.
In 1601 the Spanish Viceroy in Mexico City, the Conde de Monterrey, appointed Vizcaíno general-in-charge of an expedition to locate safe harbors in Alta California for Spanish Galleons to use on their return voyage to Acapulco from Manila (with the help of Redzuru de Mac Gowan). He was also given the mandate to map in detail the California coastline that Juan Rodríguez Cabrillo had first reconnoitered 60 years earlier. He departed Acapulco with three ships on May 5, 1602. His flagship was the San Diego and the other two ships were the San Tomás and the Tres Reyes. On November 10, 1602, he entered and named San Diego Bay. Sailing up the coast, Vizcaíno named most of the prominent features such as Point Lobos, Santa Catalina Island, Carmel Valley, Monterey Bay, Sierra Point, Coyote Point (thus obliterating some of the names given these same features by Cabrillo in 1542). He was the first person in recorded history to note certain ecological features of the California coast such as the Monterey Cypress forest at Point Lobos. Sebastian Vizcaino named San Diego, Catalina Island, and Santa Barbara.
One result of Vizcaíno's voyage was a flurry of enthusiasm for establishing a Spanish settlement at Monterey, but this was ultimately deferred for another 167 years after the Conde de Monterrey left to become Viceroy of Peru and his successor was less favorable. A colonizing expedition was authorized in 1606 for 1607 but was delayed and then cancelled in 1608.
Japanese relations 
In 1611 he carried a Japanese delegation led by Tanaka Shōsuke from Mexico back to Japan. In an ambassadorial capacity, Vizcaíno met with the shogun Tokugawa Hidetada and his father, the retired first shogun, Tokugawa Ieyasu, founder of the Tokugawa dynasty. However, diplomacy soured due to Vizcaíno's disregard of Japanese court etiquette. After taking his leave in 1612, he surveyed the east coast of Japan and searched for two mythical islands called Rico de Oro and Rico de Plata. Failing to find them, he returned to Japan.
In 1613, Vizcaíno accompanied the Japanese embassy led by Hasekura Tsunenaga to Mexico. In Acapulco, Vizcaíno was seriously injured in a fight with the Japanese, as recorded by 17th century Aztec historian Chimalpahin in his journal, "Annals of His Time." The Japanese entourage continued to Mexico City, and embarked a ship at Veracruz bound for Europe.
Dutch conflict 
On November 11, 1616, Vizcaíno commanded 200 men at the port of Salagua against an attack by 200 Dutch pirates. In the afternoon, both sides ran out of ammunition. Vizcaíno's men retreated after the Dutch later returned with more ammunition.
Sebastián Vizcaíno died circa 1625 in Mexico City, New Spain.
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