Larvae of Chaoborus flavicans (Diptera: Chaoboridae) are common in various lakes and are important members of plankton communities. To assess gene flow between lakes, we sampled several populations throughout Europe. To explicitly test whether gene flow is higher within regions than between regions, we examined four regions each containing several populations. For a detailed analysis of regional gene flow, 12 populations within a region in North Germany were analysed. Allozymes and mitochondrial restriction fragment length polymorphism (RFLP) were used to estimate the relative amounts of gene flow. Results indicate that most of the dispersal in C. flavicans takes place between lakes within regions. Therefore, the population genetic structure of C. flavicans sets this species apart from other planktonic organisms, which are mainly passive dispersers and display low gene flow between lakes within regions. Consequently, these data are the first evidence that C. flavicans may form an important link between lakes within regions. Local adaptation within lakes may be decreased because of these processes, and the role of C. flavicans as a biomonitor of local lake conditions needs to be carefully reinvestigated.