Like many other cities and towns in San Diego, San Marcos too was a ranching area where settlers came in small numbers. The place was discovered by some Spaniards belonging to the San Luis Rey Mission. It is believed that the Mission people found the area on the feast day of St. Mark back in 1797. Initially, the town was named “Los Vallecitos de San Marcos”, which means the “Little Valleys of St. Mark”. Later, the area was integrated as one of the many ranchos of California. In 1840, this rancho was allotted to Jose Alvarado. After Jose died, the rancho was sold to other people.
Finally, one Major Gustavus Merriam arrived in this area and settled here permanently. Thanks to the Major’s effort, the area saw some development and began to be called San Marcos. German and Dutch immigrants started to enter into the area during the 1880s. A post office and a couple of stores were established as the number of settlers in the area grew. Finally, the San Marcos Land Company bought this area and segregated the area into tracts. After this, more people began to purchase home in this area and settled here. From the time the water of the Colorado River was diverted here, the town witnessed a rapid phase of growth. The town also became quite popular for two products – wine and honey.
By 1970, the area had attracted more permanent settlers. The population of the town at that time was between 3000 – 4000. As per 2010 census, the population of San Marcos was close to 84,000. The town was incorporated on January 28, 1963.