Several studies have grouped the A. mellifera subspecies into five lineages (A, M, C, O and Y). Honey bees occurring in the Iberian Peninsula are considered a particular subspecies, named Apis mellifera iberiensis, originated by natural hybridization among lineages A (African) and M (western European). This study seeks to identify the level of introgression of lineage C honey bees (A. m. ligustica and A.m. carnica) in Iberian honey bees potentially caused by introduction of foreign queens by carrying out a genome wide analysis using SNPs. Over 748 individuals belonging to 23 populations sampled across three Iberian transects were genotyped for 1536 SNPs. Honey bees of lineage C A. m. ligustica and A. m. carnica were used as reference populations. The level of introgression was assessed by using Bayesian clustering methods. Our results indicate that introgression of A. m. ligustica and A.m. carnica is not noticeable in all A. m. iberiensis populations.