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At the end of the last glaciation, Apis mellifera was established in northern Europe. In Italy, Apis melliferaligustica adapted to the mild climate and to the rich floristic biodiversity. Today, with the spread of Varroa destructor and with the increasing use of pesticides in agriculture, the Ligustica subspecies is increasingly dependent on human action for its survival. In addition, the effects of globalization of bee keeping favored the spread in Italy of other honeybee stocks of A. mellifera, in particular the Buckfast bee. The purpose of this study was to characterize the Italian honeybee’s population by sequencing the whole genome of 124 honeybees. Whole genome sequencing was performed by Illumina technology, obtaining a total coverage of 3720.89X, with a mean sample coverage of 29.77X. A total of 4,380,004 SNP variants, mapping on Amel_HAv3.1 chromosomes, were detected. Results of the analysis of the patterns of genetic variation allowed us to identify and subgroup bees according to their type. The investigation revealed the genetic originality of the Sicula, and in A.m. ligustica limited genetic introgression from the other breeds. Morphometric analysis of 5800 worker bees was in agreement with genomic data.