Invertebrates were collected from eight vernal pools located on Otay Mesa, San Diego County, California during March and April 1980. Two distinct pool habitats were found. Pools with a maximum depth greater than or equal to 14 cm retained water for a period of 1.5 to 3 weeks longer than the shallow pool series. A distinct species population appeared to be associated with each pool type. Three groups of species were noted, one group widely distributed among most of the pools, a second group generally restricted to the shallow pools. Possible explanations for this distribution include predator-prey interactions, life history phenomena, and water chemistry parameters.