The Port of San Francisco has been called one of the three greatest natural harbors in the world, but it took two long centuries for navigators from Spain and England to find the anchorage originally labelled Yerba Buena. The first landing place on the north-eastern tip of the San Francisco penninsula was a small rocky promentory below Telegraph Hill later known as Clark's Point that jutted into the San Francisco Bay at the line of what is now Broadway and Battery streets. The Yerba Buena Cove swept inland from the subsequently named Clark's Point to as far as Montgomery street to the west, and further south and east to Rincon Point at the south of Market area at the foot of Folsom and Spear streets.

The founding padres of Mission Dolores and the other northern California missions found the jetty at the Clark's Point a convenient landing for their commerce in hides and tallow. It is the location where Russian ships anchored for supplies of meat and grain. Early European visitors were the Raccoon in 1816 and the French frigate Artemesia in 1827.and the sloop San Luis arrived in 1841. It was the first American warship to fly the American flag in San Francisco Bay. Not long after, the Portsmouth gave a 21 gun salute and Captain montgomery came ashore and hoisted the American flag on the Mexican flagpole in the small settlement's square, later name for the Portsmouth.

The earliest development of a port in San Francisco, two and a half miles east of the Presidio, was under the Mexican regime, begun in 1835. Before this time, the port at Monterey was considered the official port of entry to California. In 1847, the first American Alcalde, Washington Bartlett, changed the name from Yerba Buena to San Francisco, "so that the town may have the advantage of the name giiven on the public map." Captain Richardson erected the first abode of a european on the hill overlooking the Bay. He became the first harbor master by appointment of the Governor Mariano Guadaloupe de Vallejo.