In order to secure pollination services and improve conservation strategies, a better understanding of factors influencing population structure of pollinator species is vital. Here, we aimed to empirically evaluate various individual‐ and population‐based statistical methods for characterization of genetic structure of the widespread dronefly, Eristalis tenax. Thirty‐five European populations, comprising 888 individuals, were genotyped at five polymorphic allozyme loci. Three Bayesian genotypic clustering approaches (STRUCTURE, BAPS and Geneland), pairwise FST estimates, analyses of molecular variance (AMOVA), principle component analysis (PCA) and Mantel tests were applied in a comparative way in attempt to reveal the patterns of gene flow that occurs at various spatial scales in E. tenax. STRUCTURE analysis and PCA results provided no evidence of conspecific differentiation. In contrast, BAPS and Geneland clustering solutions did acknowledge low but significant proportion of among‐populations genetic variation revealed by AMOVA. Similarly, pairwise FST estimates partially argue against genetic homogeneity across Europe. The lack of correlation between genetic distance and both latitude and longitude variation suggests that the flies disperse in multiple directions. Therefore, our results indicate that continued long‐range dispersal tend to homogenize populations over time, resulting in little population structure in E. tenax across the European landmass. On the other hand, significant differentiations between geographically proximate populations indicate that dispersal potential may not be realized and that gene flow patterns in E. tenax might be geographically complex. Using information from our genetic approaches will be useful for identifying patterns of migration and population connectivity across continent, which is an important issue for conservation efforts. Since E. tenax is an important pollinator, our results contribute to understanding the potential extent to which this taxon can facilitate gene flow among plant populations across natural and semi‐natural habitats, agroecosystems and urban environments. Dronefly‐mediated gene flow in plants is likely to occur over large distances and plant–dronefly conservation will require large‐scale action.