Before the first tourist found the sun and the ideal climate to establish here, San Carlos Nuevo Guaymas, was already established in its Mexican heritage with its rugged geography and ancient geology that seems to gracefully merge all of Sonora’s unique landscapes at one place. It is known from ancient times as the Konkaak (Seri) territory and had such natural elements as the sea, chains of mountains, and an inhospitable desert. The Yaqui River on the desert coast, toward the south, was a natural boundary while to the north; the Altar Desert provided a strong defensive terrain which stretched to the east to the base of the Horcasitas mountains.

San Carlos has been the witness of the pilgrimage of Indian tribes that populated the Sonoran territory long before Mexico 's Spanish conquest. They were know to not only occupy the mainland, but to also live and prosper in the closed in and protected island regions of Tiburon, San Esteban, Isla de los patos, and Alcatraz .

The Yaqui, Guaimas, and Seri Indians survived in this natural habitat, where the ocean of the Gulf of California provides nutritious food and the “Tetakawi” hill constitutes a geographical reference with mystical meaning, that as is asserted, strengthened the warlike spirit of these tribes.

During the 18th and 19th centuries, the various tribes traded corn, salt, and deerskins. In the pre-historic era, they were organized into six tribal bands and at the same time, divided into their clans, all with recognized territorial space known as the Tepocas or Salineros, the Tiotenos, the Seris (people of the desert), and the Upanguaymas.

Because of their culture, the Upanguaymas were the antithesis of what the Spanish, and later the Mexicans, needed to colonize the region. Their territory was not easy to take advantage of. The tribe did not have accumulated wealth nor did they produce enough to make the conquest profitable. In addition, the tribesmen were considered useless to be used as laborers to cultivate and serve because they lacked the necessary cultural elements for it.

In 1701 in nearby Guaymas, the Jesuit missionaries named Eusebio Fancisco Kino and Jose Ma. Salvatierra founded the San Jose de Guaymas mission several miles from the bay. In 1703, Father Salvatierra arrived at the by to supply the missions in his charge from there, proclaiming the area a Mission de Loreto dependency.

The town was abandoned and reestablished many times due to the danger that the Upanguaymas rebels presented to the Spanish. In 1767, the Viceroy Marques de Croix ordered recognition of the Guaymas bay in order to take advantage of it as a naval and trading port. Later in 1769, Don Jose Galvez decreed the foundation of Guaymas and as a result, the Upanguaymas emigrated from this area to places farther away, leaving their ancestral Guaymas territory to the newcomers.

More locally, historical maritime records attribute the name of San Carlos to a historic sailing vessel that found shelter in its Bay during the years of this Spanish conquest. This is the first known time that the name of San Carlos is mentioned in the records of navigators that visited the region. San Carlos with its seasonal pasture lands, its bays that provide shelter to sailing vessels, and its excellent sites for scuba diving and snorkeling has since established itself as a preferred place for sports boat owners, wave seeking tourists and anyone else that enjoys water sports and the sea.

San Carlos , located north of Bacochibampo Bay , was officially founded as the Comisaria de Guaymas by the initiative of Atty. Luis Encinas, the State Governor, through decree No. 26 dated on September 28, 1963 .

However, on November 4, the San Carlos community celebrates its Saint's Day, in honor of “Saint Carlos Borromeo”, Archbishop of Milan, who was born in 1538 and who died in 1584.

Carlos Borromeo was born in the Arona Castle , on the shores of the Lago Majore in Northern Italy , during times when the Catholic Church was experiencing great hardships due to the desertion of a large portion of the population for political and religious reasons.

He gained dignified and beloved stature when in 1574, the plague attacked Milan , Italy and the Archbishop, together with his priests, traveled to visit those citizens who were on their deathbed, and thus donated all of his properties, treasures and wealth for the construction of new local hospitals and for the purchase of food.