In this study, I examined the skull morphology of three color phases of the Colombian Woolly Monkey Lagothrix lugens (Primates: Atelidae). Collecting localities of museum specimens were investigated through GIS-based modeling techniques to test for geographical and ecological patterns in L. lugens populations. Statistical analyses conducted on 28 craniomandibular measurements, in combination with the assessment of discrete characters, indicated that L. lugens consists of three geographic groups. The morphotype from the highlands of the Central Cordillera (>2,000 m altitude) matches in all characters the original description of L. lugens. There is a distinct morphotype from the lowlands of the northern Amazon (Department of Caquetá) and another from the piedmonts of the eastern versant of the Colombian Andes and the isolated mountains of the Serrania de la Macarena, herein recognized as new subspecies. The presence of an intermediate form between highland and lowland divergent lineages is also interpreted as indication of effective hybridization in a narrow contact zone at the Macizo de Garzón in the southernmost range of the Eastern Cordillera.