Ecotypic differentiation is well described in the mosquito Culex pipiens, separating populations breeding in subterranean and human-made sites (hypogeous habitat) from those in open-air sites (epigeous habitat). The pattern of population differentiation observed at the Aat-1 locus has been suspected to be associated with such ecotypic differentiation via habitat-dependent selection, but this supposition is still the subject of debate in the literature. We analysed differentiation patterns for Aat-1 and another four loci among populations from both habitat types in the French Alps. We showed that the Aat-1(A) allele is favoured within hypogeous habitats but selected against within epigeous habitats. Comparisons of our results with other data reported in the literature indicate that the Aat-1(A) allele is generally evolving under habitat-differential selection, but that the precise balance of migration and selection that determines equilibrium allele frequencies varies greatly across Europe. The nature of this habitat-dependent selection, and its resulting (geographically varying) equilibrium point, are discussed in relation to the biology of this mosquito species.