Diagnosing distinct evolutionary taxa requires careful assessment of genetic, morphological, ecological, and behavioral variation within and among populations. In this study, data on phenotype (mensural and plumage coloration), genotype (mitochondrial DNA control-region sequences), and distributional projections derived from ecological niche models, were used to investigate population differentiation of North African Common Chaffinches. Results showed substantial genetic variation among populations, mostly (similar to 56 %) distributed between Libyan populations and other North African populations, rather than within populations. Isolation-by-distance analysis indicated severely restricted gene flow between populations. Historical demographic analyses indicate that population expansion began before the Last Glacial Maximum, which is consistent with ecological niche model paleoprojections; interestingly, differentiation of the Libyan population (Fringilla coelebs harterti) apparently did not take place under the last glacial conditions. Hence, although its taxonomic status must await robust testing using multilocus DNA data, this population is an important element in the conservation of bird diversity in North Africa.