The Paraguayan tufted capuchin, Cebus libidinosus paraguayanus, lives in two different areas in South America: one is the forest of eastern Paraguay to the south of the Matto Grosso in Brazil and the other is the most southern cloud Andean Forest known as Yungas of northwest Argentina and south of Bolivia. The Tambopata tufted capuchin, Cebus libidinosus pallidus lives in the north to the center of Bolivia and northwest of Matto Grosso. The objective of this study was to evaluate the phenotypic and craneometric differences between three allopatric populations, assigned to the two different subspecies: one population of C. l. paraguayanus from the Yungas region of northwest Argentina, an other one of the same subspecies from eastern Paraguay, and a population of C. l. pallidus from the south central Bolivia region of Buena Vista. The study consisted of phenotypic observation of museum’s skins and a multivariate analysis of 21 cranial measurements of specimens housed in the collections of the Museo Argentino de Ciencias Naturales and Museo Nacional de Historia Natural del Paraguay. Two phenotypes are found in the Yungas and south central Bolivian specimens each, and one for the Paraguayan population, two phenotypes were similar to each other: the Yungas C. l. paraguayanus and Bolivian C. l. pallidus. The multivariate analysis denoted light craneometric differences between the three populations. Because the Yungas capuchin shares at least one phenotype with the Buena Vista Bolivian population, and the allopatric distribution of the paraguayanus subspecies which are about 800 km apart one each other It is proposed to name all the northwest Argentina and south of Bolivia Yungas forest Capuchin as C. l. pallidus.