The original geographical distribution of the honey bees Apis mellifera is Africa, Europe, and Western Asia, from where their export throughout the world was mediated by human beekeeping activities. In recent years, many studies have been carried out, in order to better understand Apis mellifera genetic diversity, however, the genetic composition of some subspecies located in the African continent is still poorly known. The Algerian honeybee populations are currently regarded as being members of two African honeybee subspecies: Apis mellifera intermissa and Apis mellifera sahariensis. Introduction of foreign queens and migratory beekeeping practices are factors that can affect the genetic diversity of Algerian honey bees. In this context, the study of morphological characteristics is insufficient to discriminate between subspecies and to understand potential effects of beekeeping practices. To finely reconstruct the genetic structure of Algerian population and their phylogenetic relationships with other honeybee subspecies, we sequenced a population of haploid drones, each from one colony and we included, as reference populations, subspecies of honeybees from various European locations. Our genetic analysis demonstrates a clear clustering of the samples from Algeria, which are geographically isolated from the other subspecies in our dataset. Within Algerian the population, our analysis also suggests the presence of a genetic pattern characterized by continuous east-to-west and north-south gradients. The east-west gradient along the north coast and mountains demonstrates the persistence of a genetic structure within the Apis mellifera intermissa population, despite potentially high levels of gene flow that could happen following the exchange of queens and transhumance. Honeybees samples collected in more southern parts of the country showed higher genetic divergence from the other and correspond probably to Apis mellifera sahariensis subspecies colonies. The outcomes of our study should be considered in local honey bee biodiversity improvement and conservation initiatives.