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On September 28, 1542, only twenty years after the conquest of the Aztec capital Tenochtitlan, a Spanish expedition led by the Portuguese navigator Juan Rodriguez Cabrillo discovered a "landlocked and very good harbor" which he named San Miguel since it was the feast day of that saint. Cabrillo and explorers who followed him had been sent to discover a suitable port for the Manila galleons as well as to search for a northwest passage between the Pacific and Atlantic. Anchoring near the mouth of the harbor, Cabrillo's men explored the bay with a small boat.

A shore party rowed toward a congregation of Kumeyaays who had assembled, but as the Spanish neared land, most of them ran off. Only three natives remained to inspect the strange newcomers. Cabrillo's men gave these three some gifts and in sign language the Indians communicated that they knew of other strange men like them who had been seen inland. Later that night an expedition from one of Cabrillo's ships landed on shore intending to fish. The Kumeyaay regarded this as a threatening act and began attacking the party with arrows, wounding three of the Spaniards. This was the first conflict between Europeans and the native people of California. It would certainly not be the last.

The next meeting between the Kumeyaay and the Spanish, sixty one years later was less violent. On November 10, 1603, The Spanish-Basque explorer Sebastian Vizcaíno reached San Diego bay with his expedition of three ships, two hundred men, and three Carmelite friars. Since the name of his flagship was named the San Diego and the feast day of this saint was on November 12, only two days hence, he renamed the harbor San Diego. The expedition stayed ten days during which they refitted their ships, buried those crewmembers who had died from scurvy, set up a tent church and sent an expedition inland to scout the territory. During their stay their contact with the local Kumeyaay was limited to exchanges of gifts. Vizcaíno's son led a small landing party which included a priest and they somehow met an elderly Kumeyaay woman, reported to be "one hundred and fifty years old" (perhaps the Spanish misunderstood the Kumeyaay numbering system). The old woman took them to a nearby village where they were given some small animal skins as a gift. Whatever residual memory of the violence of the first encounter among the Kumeyaay, some were willing to allow these strangers to visit their homes and even to reward them with valuable gifts.