Previous studies on the geographical distributions of both shell polymorphisms and mitochondrial haplotypes in Cepaea land snails have suggested varying contributions of natural selection, random genetic drift and population history to the origin and persistence of variation. We combine previous studies of polymorphism within two species of Cepaea, with new molecular data from two mitochondrial genes. The distributions of mitochondrial variants suggest that elements of population history may have been influential in creating patterns of diversity. However, some patterns of amino acid substitution that are found in a protein coding gene are also consistent with the action of diversifying selection. This suggests the possibility that in addition to stochastic processes such as repeated founder events, local extinctions and random genetic drift within a structured population, adaptive molecular change may have affected mitochondrial diversity. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 87, 167–184.