Recent evidence suggests a rise in the importation of non-native honey bee subspecies into Ireland with an associated potential rise in hybridisation followed by introgression. The purity of the Apis mellifera mellifera (A. m. mellifera) population in Ireland, given its decline elsewhere in Europe, makes the Irish population a very important biodiversity, and food security, resource that will also play an important role in conserving the genetic diversity of A. m. mellifera. To investigate if the Irish A. m. mellifera population can be distinguished from other European populations and to assess the introgression levels within Irish honey bees, we sampled 30 worker bees from each of 153 honey bee colonies for a pool-sequencing analysis. The assembled genomic data, also including pool sequencing data from other European studies, allowed us to confirm that pure Irish A. m. mellifera colonies are distinct from other A. m. mellifera populations and that introgression has become a serious issue.