The city was founded in 1701 by missionaries Francisco Eusebio Kino and Salvatierra, who built the Mission of San José de Guaymas 10 kms (6 miles) north of today's city.

In 1703 father Salvatierra arrived to Guaymas to provide from there the missions at his charge. The zone was constituted as a dependency of the Mission of Loreto. The town was abandoned and reestablished in several occasions due to the danger Seri natives represented. In 1767, the viceroy Marqués de Croix ordered the recognition of Guaymas Bay, aiming to use it during the military operations of the “Sonora expedition”.

In 1769, Don José Gálvez made official the Foundation of Guaymas.

In 1811 they authorized the commercial maritime traffic in the port; in 1814 the Spaniard courts inhabited here for the national commerce and in 1823, the maritime custom was established. In 1825 it was given to Guaymas the Municipality category.

In 1837 Guaymas was confirmed as a heavy traffic port. On July 13th, 1854, General Jose María Yañez leaded the defense of Guaymas against the French filibuster Count Gaston Rousset de Boulbon who wanted to take over the place. On July 13th, 1859 the title of “city” was given to Guaymas.

In 1925 the first port facilities were built in Punta de Lastre.

By 1954 the commercial activities started to have a relevant role so the wharf and the fiscal patio were built.
In 1961 PEMEX wharves for unload fluid, combustible, and tanker supply were built.

By 1964 two important projects were done at the port: the National dock by the Navy Secretary and the silos for grain exportation constructed by the National warehouse for deposit.

In 1972 Santa Rosalía city in Baja California became linked to Guaymas with the construction of the ferry wharf. Fishery activity decentralization also started with the construction of the “Sanchez Taboada” Industrial Fishery Park.

In 1980 this zone developed greatly due to technical innovations and economy growth. By that time, big private companies started moving their products by sea.