We examined morphological and genetic data for Chirostoma grandocule, the most abundant silverside fish from Lake Pátzcuaro, Michoacán, México, as part of a larger project to clarify the genetic structure of the genus. We analyzed 19 morphometric, 8 meristic, and 11 putative enzyme-coding loci from C. grandocule samples from two different localities within the lake during three different years (Janitzio 1996, 1999, and Ichupio 1997). Because morphometric attributes were all correlated, scores derived from reciprocal averaging analysis were used to describe the variation in fish morphology. Discriminant analysis using 10 morphometric and 8 meristic variables revealed significant differences between samples (Janitzio and Ichupio, χ² = 558.4 and 531.5, P < 0.001, respectively). The utilization of morphometric features for the reclassification of organisms into the site of origin was highly effective (x̄ = 98.2%). Allozyme data resolved seven polymorphic loci (P_0.99) and levels of heterocigosis that ranged from 0.0134 to 0.0319 (x̄ H_e = 0.0234). Weir and Cockerham's F-statistics provided evidence of low but significant heterogeneity between sites and years (jackknifed θ_S = 0.0252, SD = 0.0126); a pairwise comparison of θ_S values revealed that the sample from Ichupio was highly distinct compared to the samples from Janitzio (0.0400 vs. 0.0033, P < 0.05), indicating intra-lacustrine differentiation between the north and south samples. Genetic co-ancestry distances between samples ranged from 0.0154 to 0.0341. The genetic and morphometric variation detected in C. grandocule's samples are discussed in the light of differences in sex ratio and of the contrasted environmental and physio-geographical intra-lacustrine conditions.