Geographical patterns of morphological variation in small mammals are often associated with environmental factors. The southern red‐backed vole Myodes gapperi is a widespread and abundant small mammal in Canada, occurring in environments as diverse as mixed‐wood forests and taiga. First upper molars and skulls from nine populations of southern red‐backed voles distributed across three ecozones and approximately 10° of latitude were analysed by means of geometric morphometric techniques, and their relationships with environmental variables were examined. A weak, non‐linear trend of size increase towards higher latitudes was observed in voles' skulls. Environmental variables appeared to be important drivers of shape differentiation among populations from the three distinct ecozones analysed. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112, 204–218.