The honeybee, Apis mellifera L. is an ecologically and economically important insect species. Recent honey bee losses causing decline of bee diversity is found alarming for the pollination of both wild plant biodiversity and crop production. Therefore, determination of genetic diversity of honey bee populations is essential and will provide a valuable resource for conservation purposes. Twenty Random Amplified Polymorphic DNA (RAPD) primers were used to assess the genetic diversity in 720 worker bees collected from 360 colonies of 25 provinces in Turkey. Ten out of twenty primers produced 105 reproducible, bright bands, all were polymorphic. Mean genetic diversity values ranged between 0.035 and 0.175, coefficient of gene differentiation (G(ST)) values were estimated as 0.060 to 0.441, and the private band patterns reflected a high level of genetic variation. Analysis of Molecular Variance (AMOVA) partitioned the total genetic variation as 60% within, 40% among populations. The Mantel test did not reveal significant correlation between the genetic and geographic distances. First three Eigen values of principle coordinate analysis explained 63% of total variation, 27, 21, and 15% for the first, second and third respectively. The cluster analysis showed that the honey bees of Thrace region of Turkey and an island at a short distance were clustered together. The other two populations from southeastern Anatolia which belong to African lineage according to mitochondrial DNA analysis formed a separate cluster and rest of the populations which belong to north Mediterranean branch (C lineage) formed the third cluster. The results showed that genetic variability of honey bee populations from Turkey are determined using RAPD markers and provide information for future management and conservation plans.