Mandibles of yellow-necked mouse (Apodemus flavicollis) were used to explore modularity. We tested a biological hypothesis that two separate modules (alveolar region and ascending ramus) can be recognized within the mandible. As a second research goal, we compared two different morphometric procedures under the assumption that methodological approaches that use either geometric or traditional morphometric techniques should give similar results. Besides confirmation of the predicted hypothesis of modularity, the application of both approaches revealed that: 1) Modularity was somewhat more evident when it was analyzed on the asymmetric (fluctuating asymmetry, FA) than on the symmetric (individual variation) component of variation; 2) There is correspondence in the patterns of individual variation and FA, which indicates that integration of mandibular traits among individuals is primarily due to direct developmental interactions and 3) Allometry does not obscure the hypothesized modularity for individual variation or for FA. In addition, traditional morphometric method allowed us to check if allometry influenced each module to the same extent, and to conclude that the ascending ramus is more heavily influenced by general size than the alveolar region. In studies of modularity, differences in methods can lead to discrepancies in the results, and therefore some caution is required when comparing findings from different investigations. The substantial agreement between our results provides evidence that, when considering two-module organization of the mouse mandible, direct comparison among studies that use the methods applied herein is, in great part, reliable.