Chaoborus is of great interest to many freshwater ecologists. The adults can become pests in certain areas in North America and the larvae are an important food source for fish. In this preliminary study, we identified variable microsatellite loci in three species: Chaoborus astictopus (H _E = 0.52-0.76), Chaoborus americanus (H_E = 0.46-0.80) and Chaoborus punctipennis (H_E = 0.66-0.81). Using a biotin/streptavidin capture technique of repetitive sequences in a 96-well format, we obtained microsatellite-enriched genomic libraries for all three species and identified six polymorphic microsatellite markers for each species. None of the primers did yield a polymerase chain reaction fragment in a cross-species test.