Corals in marginal reef habitats generally exhibit less bleaching and associated mortality compared to nearby corals in more pristine reef environments. It is unclear, however, if these differences are due to environmental differences, including turbidity, or genomic differences between the coral hosts in these different environments. One particularly interesting case is in the coral genus Porites, which contains numerous morphologically similar massive Porites species inhabiting a wide range of reef habitats, from turbid river deltas and stagnant back reefs to high-energy fore reefs. Here, we genotyped 172 Porites corals from river delta and adjacent fore reef populations on Guam using ddRAD to assess the extent of genetic differentiation among massive Porites corals in these two contrasting environments and throughout the island. Phylogenetic and population genomic analyses identify seven different clades of massive Porites, with the two largest clades predominantly inhabiting river deltas and fore reefs, respectively. No population structure was detected in the two largest clades, and Cladocopium was the dominant symbiont genus in all clades and environments. Overall, river deltas on Guam host a distinct massive Porites species compared to its fore reefs, yet these corals host the same symbiont genera. In a broader context, the perceived bleaching resilience of corals in marginal reef environments may therefore be attributed to interspecific differences between morphologically similar species, in addition to potentially mediating environmental differences. Marginal reef environments may therefore not provide a suitable refuge for many reef corals in a heating world, but instead host additional cryptic coral diversity.