The inshore Tropical Eastern Pacific (TEP) comprises two major biogeographic provinces, the Cortez Province and Panamic Province, which are distinguished mainly by environmental differences between equatorial and subtropical regions. It is important to evaluate the influence of these environmental differences in limiting the connectivity of populations of fishes inhabiting both provinces and therefore shaping the phylogeographic patterns along the inshore TEP. Here, we used analyses based on sequences of the mtDNA control region to identify phylogeographic patterns of two snapper species, Lutjanus guttatus and L. peru, found in the coastal TEP. In both species, we found high levels of genetic diversity and a lack of genetic differentiation—as measured by both genetic fixation and genetic differentiation indices—between populations from the Cortez and the Panamic provinces. Our results suggest no significant effect of environmental differences between equatorial and subtropical waters in these two provinces on genetic differentiation, which may be explained by oceanographic features that promote larval dispersal and gene flow.