The divergence of signals used in sexual selection and species recognition is thought to play an important role in speciation. As such, the striking diversity of dewlap color in Anolis lizards may have contributed to the diversification of this species-rich group. Whether the dewlap acts as a reproductive isolating barrier however remains unclear. We tested the prediction that the degree of dewlap divergence between the two closely related and highly polymorphic Hispaniolan trunk anoles Anolis distichus and Anolis brevirostris is correlated with genetic divergence and the frequency of hybridization in nature. We use integrative analyses of dewlap color variation and molecular genetics to investigate two pairs of localities where the species co-occur, including one pair of localities where the two species exhibit dissimilar dewlaps and a second pair of localities where they have similar dewlaps. At one site where species share similar dewlap coloration, we found evidence of hybridization and lower levels of genetic differentiation. At all other localities, however, including another site where species share a similar dewlap color, the species were genetically divergent with little evidence of mitochondrial and nuclear gene flow. Together, our results suggest that dewlap color is not consistently associated with reproductive isolation at the species level. Instead, site-specific factors may influence the dewlap's role in maintaining species boundaries.