The town of San Isidro was created by virtue of Republic Act No. 4744 enacted by the Philippine Congress on June 18, 1966. It started operating as a local government unit on January 1968. Its founder and the first mayor was Vicente Yu, Sr.
San Isidro is largely planted with coconut, with much of its agricultural industry focuses on the production of copra. There are currently efforts to further diversify the output of the municipality's coconut-based industry from copra to other value-added coconut products such as coco-oil (which can be used as a fuel additive) and coco-coir. In 1992, a Crop Diversification Program of the local government unit (LGU) was implemented with mango as "export winner". In 1998, the town commenced its first Mango Festival as an indicator of the prominence of this high yielding fruit. Farmers are also engaged in growing the popular banana (cardava). Despite this, farmers still experience difficulties in increasing their income due to lack of agricultural technology specially those farming in the upland areas.
The aggressive anti-illegal fishing efforts of the LGU decreased dynamite fishing and able to establish fish sanctuaries in San Isidro waters. Most of the fishermen in this town used paddle-boat than motorized boat in fishing.
The municipality's seascape offers potential marine-based recreational industries, as its marine reserves can provide world-class and magnificent underwater adventures on the virtually undisturbed Tinaytay and Burias reefs a few kilometers offshore. In addition, its scenic nature spots include beaches untouched by urban development; the cascading Cawa-cawa Stepped Falls, and the 12 km² Pygmy or Bonsai forests in the thickly forested highlands of the municipality.