In the megadiverse conservation hotspot of the Philippines, biodiversity is not uniformly distributed throughout the archipelago, but hierarchically partitioned into islands and island groups that were conjoined during the mid- to late-Pleistocene. Few species groups are widely distributed throughout the archipelago, but some exceptions exist, such as the common scincid lizards of the Sphenomorphus jagori complex (including S. jagori, S. coxi, and S. abdictus). Using mtDNA haplotype data we test biogeographic and taxonomic predictions in these abundant, large-bodied, forest floor lizards and arrive at conclusions that differ significantly from both past, and current, appraisals of species diversity. In contrast to expectations based on existing taxonomy (three species, each with two subspecies), we find evidence of at least eleven highly divergent species lineages diagnosed by haplotypic variation. Each lineage corresponds to a biogeographically circumscribed distribution (i.e., isolated islands or geological components of islands), suggesting lineage cohesion and allopatric differentiation. Parametric bootstrapping tests reject taxonomic and biogeographic hypotheses and suggest a complex pattern of unpredicted relationships. Only one of the former species (S. jagori) appears as a monophyletic entity (including four allopatric, highly divergent lineages that we suspect may represent evolutionary species), and the remaining species are paraphyletic, necessitating a comprehensive future taxonomic revision. The pattern of biogeographic provincialism and hidden cryptic species diversity detected here leads us to suspect that even the most common, presumably well-studied, and widespread species complexes in the Philippines are in need of thorough analysis with modern genetic and phylogenetic techniques. Such studies of speciation genetics in these common, widely distributed groups may lead to a better understanding of the genetic underpinnings of biodiversity, allow for an enhanced appreciation of the evolutionary history of this model island archipelago, and enable more informed conservation planning in a global biodiversity hotspot.