Conservatism of ecological niches can cause geographical ranges or the formation of new species to be constrained, and might be expected in situations where strong trade-offs result in ecological specialization. Here we address the flexibility of resource use in European crossbills by comparing the ecological and genetic similarities between four Mediterranean and three northern European crossbill populations, all specialized in feeding on a different resource. We used sequence data of one mitochondrial and two nuclear genes from between 211 and 256 individuals. The northern crossbills were genetically too similar to infer which population was more related to the southern ones. Crossbills from the island of Mallorca showed genetic signatures of a stable and isolated population, supporting their past treatment as a locally (co)evolving taxon, and seem to have evolved from an ecologically distinct ancestor. Previous studies in other populations also suggest that genetic similarity does not predict morphological and resource similarity. We estimate that the divergence of all western European crossbills has occurred within the last 11 000 years. Overall, it appears that crossbills can diversify rapidly and with little niche conservatism, but that such potentially reproductively isolated specialists are evolutionarily short-lived. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109, 908–922.