Characterising the genetic diversity of populations allows to better understand their demographic history and their adaptation to selective pressures. In honey bees, this characterisation is facilitated by a relatively small genome size, but is hindered by the fact that often the unit of observation and sampling is the colony rather than a single individual. Moreover, performing large scale genetic analyses of honey bees is a real challenge, due to the specific reproduction mechanism including multi-male insemination, making the genotype of a bee colony a mixture of contribution from the queen and the mating drones. In this work we propose an approach to characterise the genotype of a colony based on pool sequencing of worker bees. We introduce statistical models for the analysis of pool sequence data allowing to reconstruct jointly individual queen genotypes of colonies and allele frequencies in bee populations. We demonstrate the performance of our approach using data on 1500 colonies collected throughout three years within the FranceAgriMer funded, BeeStrong project. Population admixture, in terms of queen sub-species composition, validation was accomplished using information on geographical and sociological organisation of the beekeepers. In addition to a better understanding of the population dynamics of honey bees, our approach to genotyping bee colonies promises to facilitate the genetic analysis of complex traits, and can be used for genome wide association studies on phenotypes of interests, for instance to assess Varroa resistance in honey bee populations.