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Because patchiness of food sources or nesting opportunities frequently limits gene flow, specialists often exhibit distinct population structures in fragmented habitats. We studied the influence of habitat fragmentation on population structure in the solitary bee Andrena vaga, an early spring species that nests exclusively in sandy soil and feeds strictly on willows (Salix spp.). Because the homogenous habitat of the German floodplains, where the species was studied previously, resulted in the species’ weak population structure, we expected more structured populations in central Europe, where the sandy soils essential for nesting are highly fragmented. We analysed 387 females from 21 localities in the Czech Republic and Slovakia using nine microsatellite loci, and we inferred population structure using landscape genetics and Bayesian clustering methods. Contrary to our expectations, habitat fragmentation did not result in increased genetic isolation at the localities; however, two differentiated groups of localities, separated by a wide clinal zone of admixture, were detected within the study area. The observed pattern suggests that dispersive ability of A. vaga compensates the species dependence on unstable fragmented habitats. We propose that the population structure may mirror a secondary contact formed by the expansion of two populations that had been separated in the past. We emphasise the necessity of knowing the studied species’ population history before making conclusions concerning correlations between habitat and population structure, especially in areas of known suture zones created by the secondary contact of populations expanding from separate refugia.