Citril finches Carduelis c. citrinella and Corsican finches Carduelis c. corsicana represent two closely related forms, endemic to European mountains and some Mediterranean Islands. Their taxonomic status has recently been disputed based on the results from mitochondrial genes. We show that the use of different genetic markers may lead to different results in these two putative species. Using the mitochondrial ATP8+6 we found a clear difference between C. c. citrinella and C. c. corsicana (3.2%) suggesting a divergence time of 1.2MYR. In contrast, no clear difference was found using two nuclear genes. The mismatch between the different markers suggests that the separation of C. c. citrinella and C. c. corsicana is likely to be a rather recent event, involving bottlenecks, which have enhanced the divergence in the mtDNA. Our results call for caution when using mtDNA alone for assessing times of divergence and rates of evolution. We did not find any support for the view that C. c. corsicana is more related to Carduelis carduelis than C. c. citrinella as proposed by previous studies.