Recent evidence of genetic homogeneity across morphologically diverse crossbill taxa Loxia spp. suggests that strong directional natural selection sustains morphological differences. If so, we would expect that, in sympatry, persistent crossbill morphs will be associated with the ecological circumstances that select for particular features. Here we report on a field study of niche differentiation in sympatric crossbills, showing correlation between bill size and habitat use, foraging and movements. In Deeside, north-east Scotland, crossbills occupied three ecological niches. Small-billed birds L. curvirostra were itinerant and migratory. They switched between conifer species in relation to the phenology of cone ripeness, feeding on spruce or larch from summer through winter and Scots Pine Pinus sylvestris in spring and early summer. Large-billed birds L. pytyopsittacus were more sedentary, feeding on pine seed year round in semi-natural pine forest. Birds with intermediate bills L. scotica were also sedentary but switched seasonally between conifer species. Deeside crossbills thus occupied three niches in line with the current designation of three species, but in the study years (1990–1997) there was no shortage of conifer seed and no evidence of strong selection for optimal bill size. Bill sizes did not fall precisely into three distinct modes so other factors were involved. These could have included the immigration of two sizes of L. curvirostra, and introgression (and possibly phenotypic plasticity) amongst the more sedentary larger-billed birds. The origin of L. scotica is discussed within the context of novel habitat, introgression, niche shift and competition for pine seed.