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The California roach Lavinia symmetricus is a small cyprinid native to Central California. Populations of roach are presently isolated from one another due to degradation of stream habitats between them. We examined eight populations, each from a tributary system of the San Joaquin River, to determine if morphological differences existed among them. These tributaries are now isolated from one another by dams or areas of unsuitable habitat. We found significant differences among drainages for all of the characters studied. Discriminant analysis classified 70% of the individuals to the correct drainage. The differences were not clinal because adjacent drainages were not grouped together in discriminant space. The most distinct population was as different from a nearby population (36 stream km) as from populations from other more distant tributaries and could possibly merit subspecies status. These results suggest that each population has been isolated long enough to develop morphological adaptions to local environmental conditions. With one exception, the differences among the populations were too small for formal taxonomic recognition but suggest that management should focus on preserving local populations throughout the species’ range, rather than scattered populations in a few reserves. This policy would serve to protect the genetic diversity of California roach, local aquatic habitats, and other even more poorly known species.