Honey bees (Apis mellifera L.) are the primary commercial pollinators across the world. The subspecies A. m. scutellata originated in Africa and was introduced to the Americas in 1956. For the last 60 years it hybridized successfully with European subspecies, previous residents in the area. The result of this hybridization was called Africanized Honey Bee (AHB). AHB has spread since then, arriving to Puerto Rico (PR) in 1994. The honey bee population on the island acquired a mosaic of features from AHB or the European Honey Bee (EHB). AHB in Puerto Rico shows a major distinctive characteristic, docile behavior, and are called gentle Africanized Honey Bees (gAHB). We used 917 SNPs to examine the population structure, genetic differentiation, origin and history of range expansion and colonization of gAHB in PR. We compared gAHB to populations that span the current distribution of A. mellifera worldwide. The gAHB population is shown to be a single population that differs genetically from the examined populations of AHB. Texas and PR groups are the closest genetically. Our results support the hypothesis that the Texas AHB population is the source of gAHB in Puerto Rico.