Aim The Lesser Sunda Islands are situated between the Sunda and Sahul Shelves, with a linear arrangement that has functioned as a two-way filter for taxa dispersing between the Asian and Australo-Papuan biogeographical realms. Distributional patterns of many terrestrial vertebrates suggest a stepping-stone model of island colonization. Here we investigate the timing and sequence of island colonization in Asian-origin fanged frogs from the volcanic Sunda Arc islands with the goal of testing the stepping-stone model of island colonization. Location The Indonesian islands of Java, Lombok, Sumbawa, Flores and Lembata. Taxon Limnonectes dammermani and L. kadarsani (Family: Dicroglossidae) Methods Mitochondrial DNA was sequenced from 153 frogs to identify major lineages and to select samples for an exon-capture experiment. We designed probes to capture sequence data from 974 exonic loci (1,235,981 bp) from 48 frogs including the outgroup species, L. microdiscus. The resulting data were analysed using phylogenetic, population genetic and biogeographical model testing methods. Results The mtDNA phylogeny finds L. kadarsani paraphyletic with respect to L. dammermani, with a pectinate topology consistent with the stepping-stone model. Phylogenomic analyses of 974 exons recovered the two species as monophyletic sister taxa that diverged 7.6 Ma with no detectable contemporary gene flow, suggesting introgression of the L. dammermani mitochondrion into L. kadarsani on Lombok resulting from an isolated ancient hybridization event 4 Ma. Within L. kadarsani, the Lombok lineage diverged first while the Sumbawa and Lembata lineages are nested within a Flores assemblage composed of two parapatrically distributed lineages meeting in central Flores. Biogeographical model comparison found strict stepping-stone dispersal to be less likely than models involving leap-frog dispersal events. Main conclusions These results suggest that the currently accepted stepping-stone model of island colonization might not best explain the current patterns of diversity in the archipelago. The high degree of genetic structure, large divergence times, and absent or low levels of migration between lineages suggests that L. kadarsani represents five distinct species.