There are three breeding taxa of crossbills in highland Scotland, the common crossbill Loxia curvirostra, parrot crossbill L. pytyopsittacus and endemic Scottish crossbill L. scotica. These taxa show no genetic differentiation in neutral DNA (microsatellites and mitochondrial DNA), but do show some differentiation in morphology and have distinct calls. Mating patterns and bill size inheritance were examined to test four different hypotheses for their genetic similarity: (1) the three taxa belong to the same species and differences in bill sizes are caused by phenotypic plasticity, (2) the taxa are a result of genetic polymorphism at a single locus, (3) the taxa largely act as species but occasionally cross-breed, such that gene flow results in genetic homogenisation of part of the genome, and (4) the taxa are fully reproductively isolated species but diverged only recently, such that insufficient time has passed for neutral DNA to differentiate by genetic drift. Hypotheses 1 and 2 could be excluded because wild crossbills mated assortatively with respect to bill depth (a measure of bill size) and bill depth was highly heritable; narrow-sense heritabilities of 0.58 for female and 0.71 for male Scottish crossbills. Only two of 46 pairs (4.3%) were not assortative by bill size. Pairing was strongly assortative by flight calls (50 out of 52 pairs, 96.2%) and excitement calls (88 out of 93 pairs, 94.6%). Therefore, the three crossbill taxa do not cross-mate freely, nor do they seem totally reproductively isolated (excluding hypothesis 4). Thus, the results mostly favour hypothesis 3. The small amount of gene flow among crossbill taxa may contribute to the lack of genetic differentiation in neutral DNA. However, this appears to be insufficient not to classify them as species, as long as the calls can be regarded as diagnostic.