Pacific island land snails are among the most imperiled animals on Earth, which elevates the practical conservation importance of their systematics and biogeography. The Micronesian endemic land-snail genus Semperdon Solem, 1983 is composed of five described species from Belau and the Mariana Islands. Although these species are readily identifiable based on morphology, the existence of cryptic lineages within described species on Belau was proposed in the only systematic treatment of Semperdon and its relatives. New specimens of Semperdon species from Belau allow a rare opportunity to test for putative cryptic lineages in this severely threatened genus and to examine phylogeographic patterns in a non-hotspot archipelago. During this study, species delimitation within the Belau Semperdon species was analyzed using one distance-based (ABGD) and two tree-based (single-threshold GMYC and bPTP) molecular species delimitation methods and DNA sequence data from cytochrome c oxidase subunit I (COI) and the nuclear Internal Transcribed Spacer 2 (ITS2) region. In addition, a TCS network was used to explore the relationships of COI and ITS2 haplotypes and newly identified cryptic lineages. Based on these results, the first morphologically cryptic lineages are reported from Pacific endemic Charopidae. The strong phylogeographic structuring and exceptionally high mtDNA divergence on the archipelago suggests highly insular populations over relatively short geographic distances, roughly corresponding to smaller island groups within the archipelago. Finally, protection for island groups closest to human habitation and further survey efforts are recommended to mitigate extinction in this genus.