We review the species of the Brachymeles bonitae Complex (B. bonitae and B. tridactylus) and describe an additional two new species in this highly specialized, limb-reduced, endemic Philippine clade of fossorial lizards. For more than 4 decades, B. bonitae has been recognized as a single “widespread” species, a perception that has persisted as a result of limited sampling and similar overall morphology (body sizes, scale pigmentation) among populations. However, on the basis of new collections we note consistent morphological differences between populations, and our new data build on previous observations, allowing us to utilize newly defined character state differences for the purpose of delimiting unambiguous boundaries between species. Here, we use morphological and molecular data to define species limits in B. bonitae and its close relatives. Our data indicate that the “widespread” species B. bonitae is actually a complex of four distinct evolutionary lineages, several of which are not each others' closest relatives. The taxa we define possess allopatric geographic ranges (biogeographically supporting our taxonomic conclusions) and differ from their congeners by several diagnostic characters of external morphology. We conclude that each, therefore, should be recognized as full species in accordance with lineage-based species concepts. Species diversity in the genus has doubled in the last 4 yr, with newly described taxa increasing the total number of species of Brachymeles to 38.