Morphological diversity was analyzed in pumpkinseed sunfish (Lepomis gibbosus) between a lake (40.5 ha) and a pond (4 ha) at the Huyck Preserve and Biological Research Station in upstate New York. The hypotheses were (1) fish from the lake and pond would differ in body shape due to different biotic/abiotic factors in each water body, and (2) there would be a difference in variance in body shape between the lake and the pond due to differences in the availability of niches. Body shape variation was examined using geometric morphometrics, and parametric statistics were used to identify differences in body shape, and differences in the variance in body shape, between fish from the pond and the lake. Fish from the pond were, on average, slightly deeper bodied for a given body size; however, there was substantial overlap in variation, so this variation may not be ecologically significant even though it is statistically significant. The variance in components of body shape also differed between the pond and the lake. These results support the hypothesis that body shape, and variance in body shape, differ between the pond and the lake. The variation might have been stronger were it not for gene flow that could be preventing further ecological divergence. It is also not known whether observed patterns are due to evolutionary processes or are a result of phenotypic plasticity. Further research is needed to determine if these patterns hold when sampling across a broader range of water bodies.