The Philippine archipelago, located in the northern apex of the Coral Triangle, is known for its high diversity and endemism, both caused by a complex physical setting modelled by the long tectonic history of the archipelago and by the more recent Pleistocene sea-level fluctuations. In order to assess the influ- ences of the complex Philippines geography on benthic marine species, we conducted phylogenetic and phylogeographic analyses on 71 specimens (out 112 originally collected) of ten species of Pinnidae, sequencing two mitochondrial and two nuclear markers. Our results suggest that the Philippines is a diversity hotspot for pinnids, with all sampling sites hosting three or more species, but with marked differences in species composition in each site, indicating that most pinnids have a patchy distribution. Our data also suggest that most species exhibit high levels of genetic connectivity even over large geo- graphical distances. As previouly suggested, our data also sup- port the idea that the nominal taxon Pinna atropurpurea includes at least 2 cryptic species in the Philippines.