[3] On the eastern flank, Mine Canyon and Marron Valley separate the San Ysidro Mountains from Tecate Peak (Kuuchamaa).

[4] The Cerro San Isidro, located in Tijuana, is separated from the rest of the range by the border fence and the Rio Alamar, and forms the southern portion of the mountains.

The summit of the Cerro San Isidro reaches approximately 2,750 feet (840 m), and supports many of the same endemic and rare plants found on Otay Mountain.

[6] The native vegetation of the San Ysidro Mountains represents the coastal sage scrub of the California coastal sage and chaparral ecoregion (western faces); and plants of the California montane chaparral and woodlands ecoregion (inland).

The San Ysidro Mountains are one of the few locations the rare Tecate Cypress (Cupressus forbesii) is found.