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Expression of heat shock protein genes (Hsp) could be determinant for fish to survive an increase of water temperature due to global warming. Coastal lagoons, with their intrinsic high-water temperatures, test the resilience and adaptability of fish populations to environmental change. We analyze the variation in gene expression and genetic variation of 2 endemic Fundulus species in 2 lagoons to the north of the Yucatan Peninsula. We evaluated genetic distances between species using Hsp 70 gene sequences; our results showed low genetic differentiation between both Fundulus species and also showed individuals with high genetic variability, due to non-neutral polymorphisms. Expression of 2 isoforms of Hsp70 genes was higher in F. grandissimus than in F. persimilis. These variations are prompted by water temperature and genetic differentiation of species, induced in the fish thermal stress sensitivity. Our results suggest that both species are sensitive to thermal stress; however, populations exhibit wide genetic expression range and non-neutral polymorphisms, which could be an evidence of an adaptive process to thermal stress. This capacity of the fish populations to adapt to environmental variations could be affecting fish distribution.