The pollen beetle (Meligethes aeneus) is one of the most important insect pests of oilseed rape (Brassica napus), and extensive use of insecticides is required to protect crop yields. To meet the challenges set by agricultural demands for more sustainable production and changing climate more information about pest biology and population genetics is needed. Using genomic Amplified Fragment Length Polymorphism (AFLP) analysis, DNA polymorphism was studied in 14 field populations of pollen beetles, collected during 2004 in six European countries (Denmark, France, Finland, Germany, Sweden, and UK). Using one primer combination 410 polymorphic DNA fragments were obtained based on analysis of single beetles. AFLP profiles were analysed with similarity measures using the Nei and Li coefficient and dendrograms generated. Dendrograms constructed from distance matrices revealed clustering by population origin and assignment analysis generally supported the genotype classification. Principal component analysis of the fourteen groups resulted in wide dispersion but also connections between some groups. Statistical analysis using AMOVA showed that the levels of genetic variation within populations explained most of the variation. Migrant analysis suggested a low level of gene flow between pollen beetle populations at different geographical locations indicating little long range dispersal of pollen beetles. However, a Mantel test found no correlation between genetic and geographical distance. Apparently genetic differentiation among populations has a complex background and may involve factors such as local adaptation and founder effects.