Isotopic variation in northern and southern hard clam (quahog) shells is used in studies including paleoecology, paleoclimatology, and archaeology. It is unknown, however, whether species-specific isotopic differences exist. Three genotypes—Mercenaria mercenaria, M. campechiensis, and their natural hybrid form—are found in coastal Florida waters and differentiation of genotypes can be difficult to determine morphologically. This issue may be problematic when using archaeological shells as paleoclimate archives, because genetic analysis cannot be done on such specimens. Their co-occurrence in coastal Florida waters provides a unique opportunity to study whether all three genotypes of modern individuals record the same environmental information preserved as variation in oxygen and stable carbon isotope ratios. A random sample of 49 individuals collected alive at the same time and from the same locality in Pine Island Sound were classified to genotype using allozyme electrophoresis. Three juveniles from each genotype were selected for isotopic analysis to control for ontogenetic effects. Timing of growth increment formation inferred from oxygen isotope ratios reveals similar overall patterns wherein dark (slow growth) increments formed in mid- to late spring and light (fast growth) increments formed in late fall. Results of the mixed model ANOVA (analysis of variance) indicate that no significant species-related differences exist in the variation of oxygen and carbon isotope ratios, although the Kolmogorov-Smirnov goodness-of-fit test detected a systematic difference among δ13C values of M. mercenaria and M. campechiensis comparison and M. mercenaria and the hybrid shell comparison. Any genotype or combination thereof is, thus, suitable for environmental and climate reconstruction using oxygen isotope ratios. The utility of carbon isotope ratios as an environmental proxy, however, remains questionable.