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Bulb mites are an economically significant pest of subterranean parts of plants and a versatile laboratory animal. However, the genetic structure of their populations remains unknown. To fill this gap in our knowledge of their biology, we set up a field experiment in which we allowed mites to colonize onion bulbs, and then determined the genetic structure of colonisers based on a panel of microsatellite loci. We found moderate but significant population structure among sites separated by ca. 20 m (FST range 0.03–0.21), with 7% of genetic variance distributed among sites. Allelic richness within some bulbs was nearly as high as that in the total population, suggesting that colonisation of bulbs was not associated with strong population bottlenecks. The significant genetic structure we observed over small spatial scales seems to reflect limited dispersal of mites in soil. [ABSTRACT FROM AUTHOR]