The aim of the present work was to investigate the relationship between canalization and developmental stability under varying environmental conditions. Three different cohorts of Mastomys natalensis (Rodentia, Muridae), displaying different growth trajectories, were analyzed by means of Geometric morphometrics. A set of 23 landmarks was digitalized on the dorsal skull of 292 specimens from Morogoro (Tanzania). Patterns of among- and within-individual (measured as fluctuating asymmetry) variation were assessed and compared among and within the three groups in order to test for the presence of a common mechanism between canalization and developmental stability. Results showed that there was no congruence between canalization and developmental stability: 1) levels of FA and among-individual variation varied in a discordant fashion, 2) no correspondence between variance-covariance matrix of among- and within individual variation was found, 3) environmental effects were able to alter the covariance structure of among- individual variation living patterns associated with fluctuating asymmetry unaffected. These findings support the view of multiple mechanisms underlying developmental buffering of shape variation.