Integration of genetic connectivity information in effective marine reserve (MR) design is important in sustaining marine biodiversity. Here, genetic connectivity based on mitochondrial DNA (mtDNA) of three reef fish species, namely Epinephelus merra (n = 67; 32 from Bolinao, 14 from Alaminos, and 21 from Masinloc), Parupeneus multifasciatus (n = 23; 12 from Bolinao and 11 from Masinloc), and Odonus niger (n = 35; 21 from Mabini and 14 from Tingloy), sampled across western Luzon, Philippines, was inferred by assessing their genetic diversity, population genetic structure, and historical demography. The results show high haplotype and nucleotide diversity in the three species. Tests for population structure indicate high gene flow and no spatial genetic structuring for the three species. Mismatch analyses suggest unimodal distribution for E. merra and P. multifasciatus, but bimodal distribution for O. niger. Even with differences in mismatch distributions, all the three species exhibit low raggedness index indicating demographic population expansion. The bimodal distribution of O. niger could be attributed to the mixing of two isolated populations. High gene flow between sampling locations implies genetic exchanges and connectivity between many small MRs and fishing grounds in western Luzon, Philippines, at a scale similar to our study. This research is among the first few to elucidate the high genetic connectivity of reef fish communities across the Philippines (here western Luzon), but it also calls for more support (i.e. government and academia) for genetic research that aims to (1) understand the maintenance of megadiversity of the country and (2) search for effective biodiversity conservation options for the coral reefs.