Despite the growing literature on the underlying factors of geographical phenotypic variation, little is known about how and to what extent biogeographical barriers in Southeast Asia have shaped morphological variation in primates. We aimed to investigate the geographical variations in skull morphology in dusky leaf monkeys by decomposing them into clinal (latitudinal), non-clinal spatial (discrete difference between regions north and south of the Isthmus of Kra), and environment-related components. We applied geometric morphometrics to measure 53 adult male specimens from 36 localities, covering the regions both north and south of the Isthmus of Kra. A linear model was used to test the effects of region (north vs. south of the Isthmus of Kra), latitude, and environmental factors (temperature and rainfall) on the size and shape of skulls. A part of variation in skull shape differed moderately between the regions in the north and south of the Isthmus of Kra, and this difference cannot be explained by latitudinal and environmental factors. However, for size and the majority of variations in shape, we detected limited contributions of region and the two environmental factors. Shape differentiation that was unexplained by latitudinal and environmental factors suggests that dusky leaf monkeys may have experienced a population division due to habitat constriction around the Isthmus of Kra. However, this divergence probably has been obscured by subsequent gene flow between populations after habitat recovery.