This study provides a quantitative assessment of the craniofacial variation among recognized species and subspecies in the Saguinus mystax species group and tests the reliability of the proposed method in detecting differences among taxa. Thirty measurements were taken of 66 tamarin specimens. We used non-parametric MANOVA to test for differentiation among species and among subspecies. Interspecific analyses showed significant variation among species, except for S. inustus. We detected significant differentiation between S. mystax mystax and S. m. pileatus, whereas no significant morphometric difference was found between S. imperator subspecies. Measurements presenting some differentiation among species were selected for subsequent analysis of variance. Univariate analyses detected significant differences among species only for three measurements. Our results suggest that the cranial morphometric variation has limited information to discriminate among the taxa in the S. mystax group. However, we cannot disregard the lack of statistical power due to small sampling in some taxa, absence of some subspecies in the analyses, or even lack of informativeness of the chosen measurements. Morphometric analyses was insufficient to demonstrate complete differentiation in Saguinus. The use of morphometric analyses should not be considered as a definitive method for taxa differentiation and delimitation in Saguinus.