Coral species are difficult to identify due to few distinct morphological features and high levels of phenotypic variation; furthermore, hybridization is thought to play an important role in coral evolution. The genus Pocillopora is one of the most abundant reef-building corals in the Pacific, yet species boundaries within this important group remain enigmatic, with conflicting interpretations of molecular data. To further examine the relationship between morphology and genetic variation, we examined in situ photographs, microscopic images, and molecular markers (ORF, CR, ITS-2) from 59 Pocillopora colonies representing a range of atypical morphologies thought to be rare or endemic to remote locations (the Hawaiian Archipelago, Johnston Atoll, Palmyra Atoll, and Howland Island). Additionally, we combined our data with previously published genetic data from the western Indian Ocean, Taiwan, the Great Barrier Reef, and the tropical east Pacific (n = 298) to examine phylogeographic relationships more broadly. Mitochondrial markers revealed six distinct clades, while nuclear data (ITS-2) resolved no clear groups due in part to intragenomic variation. Although colony-level morphology is highly variable within each mitochondrial clade, microscopic corallite-level morphology showed less variation and stronger concordance with mitochondrial groups, and one clade was found only in the Hawaiian Archipelago. These findings will assist with efforts to delineate species boundaries in the genus Pocillopora and contribute to understanding the scale of species-level variation in reef building corals. Accurate determination of species boundaries will improve conservation efforts and further our understanding of the evolution and biodiversity of reef building corals.