Objective: This study examined the intra-specific cranial morphometric variability between populations of Malacomys edwardsi from three distinct localities in Côte d'Ivoire. Methodology and results: The data set focused on 23 cranial measurements recorded on 158 skulls of M. edwardsi from Adiopodoumé (n = 43), Bolo (n = 34) and Taï (n = 81). Sexual and geographical variations were investigated using univariate and multivariate statistics. No sexual dimorphism was recorded. However highly significant morphometric differences were observed between the three populations. This study observed a longitudinal clinal size variation for five measurements. Moreover, populations from the left bank of the Sassandra River are morphometrically closer to one another than to those found on the right bank. Conclusions and application of findings: This study reveals that the three populations of M.edwardsi exhibited local morphological differentiation. Additional studies are needed to better explain the determinants of this variation (local adaptation, phylogenetic history). This is important for both the systematics and conservation of this endemic species of the West African forests.