Abstract 1 Pollen beetles Meligethes aeneus are pests of oilseed Brassica crops that are subject to intensive chemical control. Resistance to pyrethroids has been reported. Although this insect is of great economic importance, little is known about its genetic properties and population structure. 2 Amplified fragment length polymorphism (AFLP) analysis with the restriction endonuclease combination EcoRI and PstI was performed on 133 samples of groups of three pollen beetles collected during 2001–04 from five different provinces of Sweden. Both susceptible and resistant insects were studied. Using one primer combination, more than 450 polymorphic DNA fragments were obtained and, in total, four primer combinations were used for analysis. A subsample of 59 single beetles was analysed using one primer combination. 3 AFLP profiles were analysed by similarity measures using the Nei and Li coefficient and Neighbour-joining dendrograms were generated. The dendrogram built using 133 samples showed three distinct groups, each containing beetles representing one generation. Statistical analysis using analysis of molecular variance of single beetle samples showed no evidence of significant genetic difference between resistant and susceptible beetles. Instead, a clear difference between samples, depending on time of collection and generation, was observed. 4 The expected regional population structure, although statistically significant, explained little of the variation. The levels of genetic variation within populations were very high. There appears to be a high rate of gene flow between pollen beetle populations. The implications of this in the context of insecticide resistance are discussed.