Abstract. Aphid species Aphis pomi (de Geer, 1773) is oligophagous on pomoideous host plants, whilst Aphis spiraecola Patch, 1914 is a polyphagous species alternating between Spiraea spp., its primary host, and a wide variety of secondary hosts, also including pomoideous species. Despite the biological distinction, these species are difficult to separate using their morphological characters. Partial sequences of mitochondrial COI and nuclear EF-1α genes were analyzed for samples from Central and Eastern Europe, Germany, Bulgaria, Italy, Turkey, China together with available data from GenBank. Interspecific pairwise sample divergences of the COI fragment ranged from 3.1 to 4.3%. One COI haplotype of A. pomi was predominant (n = 24), with a pan European distribution. The most abundant COI haplotype of A. spiraecola (n = 16) occurred in Lithuania, Latvia, Poland, Italy, Turkey and China. Interspecific pairwise sample divergences of the EF-1α fragment ranged from 0.6 to 1.2%. Analyzed partial sequences of EF-1α were identical in A. pomi. The most abundant EF-1α haplotype of A. spiraecola (n = 14) occurred in Lithuania, Poland, Italy, Turkey and China. The length of ultimate rostral segment appeared to be the most reliable morphological character for discrimination between apple and spirea aphid species. It allowed a 100% correct identification of A. pomi (n = 143) and 91.5% of A. spiraecola (n = 94) specimens in the European samples used for the molecular analysis. The existence of A. spiraecola in the Eastern Baltic region of Europe is documented for the first time.