We use mitochondrial gene sequences to estimate relationships among Gekko populations from the northern Philippines. These data, plus morphological and biogeographical evidence, suggest that the Babuyan and Batanes island groups (north of Luzon Island) are inhabited by a minimum of six distinct evolutionary lineages, only two of which (Gekko porosus Taylor from the Batanes and Gekko crombota from Babuyan Claro) have been formally recognized as distinct species. In this paper, we provide a description of another new species, the endemic Gekko from Calayan Island. This geographically isolated species is diagnosed on the basis of a distinct color pattern, body size, scalation, and significant divergence in mitochondrial gene sequences. The new species has been found on rocky outcrops and limestone caves in forested areas and on trunks of mature forest trees ≤500 m above sea level, away from the island's coast. Given the history of geological isolation of Calayan Island and the distinctiveness of the endemic Gekko populations there, we are confident in diagnosing this gecko as a unique evolutionary lineage; it is unlikely that this species will be found on neighboring land masses. The remaining major islands of the Babuyans group (Camiguin Norte, Fuga, and Dalupiri islands) each contain similarly distinct endemic species that await description; additional surveys throughout the Batanes and Babuyan islands will be necessary to arrive at an estimate of total species diversity for this isolated gekkonid radiation.