The Icelandic redpoll Carduelis flammea islandica is one of three subspecies of Carduelis flammea. The other two are C. f. rostrata, breeding in Greenland, and C. f. flammea, widely distributed at high latitudes in both N-America and Eurasia. Recent studies on variation of the mtDNA control region and in microsatellites among C. f. rostrata and C. f. flammea mainly from Scandinavia and related species (C. hornemanni, C. cabaret) didn’t reveal clear genetic differentiation among the species. The lack of differentiation could result from introgression (hybridization has been supported by direct observations) and/or incomplete lineage assortment following recent diversification. Here we add result of the Icelandic subspecies C. f. islandica to previous analysis of the species complex to evaluate its reproductive isolation. The Icelandic subspecies is particularly interesting because of its intermediate size and colour between the two extreme forms; C. cabaret and C. hornemanni. This study includes in addition a comparison of different and highly variable genetic markers: mitochondrial (control region and COI) and nuclear introns (TGFβ2 and Fib7). Significant differences in haplotype frequencies of the mtDNA control region are observed between the Icelandic subspecies and the common redpoll (C. f. flammea). Variation in the COI reflects a geographical barrier, which describes two clades: one “mainland” and the other “arctic”. This main finding supports a previous hypothesis describing two allopatric refugias during the last glaciation period.