The integrated results of maximum likelihood (ML) and Bayesian inference (BI) analyses, principal component analyses (PCA), and a multiple factor analysis (MFA) recover a new, widely allopatric species of the Cyrtodactylus intermedius species group. Cyrtodactylus kulenensis sp. nov is endemic to the Phnom Kulen sandstone massif of the Phnom Kulen National Park, Siem Reap Province, in the lowlands of northwestern Cambodia. A phylogenetic analysis from a short read (275 base pairs) of the mitochondrial gene NADH dehydrogenase subunit 2 (ND2) from C. kulenensis sp. nov. was aligned with 1449 base pairs from all other species in the intermedius group. The analysis recovered C. kulenensis sp. nov. as the sister species to a lineage composed of populations from the widely separated hilly regions of Sa Keao and Sakaerat in eastern Thailand. Multivariate (PCA, DAPC, and MFA) and univariate analyses (ANOVA) using combinations of meristic (scale counts), mensural (morphometric), and categorical (color pattern and morphology) characters from 52 specimens encompassing all species of the intermedius group clearly demonstrate C. kulenensis sp. nov. is significantly different and discretely diagnosable from all other species in the intermedius group. This new discovery further highlights the herpetological diversity and high levels of range-restricted endemism in basin-habitat-island landscapes throughout Indochina and the continued need for field work in the landscapes that remain unsurveyed.