Because of its widespread distribution in lakes and ponds Chaoborus is of great interest to many freshwater ecologists. Interestingly some species are restricted to small fish-less water bodies, whereas other species live mostly in large lakes. To eventually test the genetic and evolutionary implications of these different lifestyles we identified microsatellite loci in three species in this preliminary study: C. obscuripes, C. crystallinus and C. flavicans. 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.