Aquatic invertebrates experience strong trade-offs between habitats due to the selective effects of different predators. Diel vertical migration and small body size are thought to be effective strategies against fish predation in lakes. In the absence of fish in small ponds, migration is ineffective against invertebrate predators and large body size is an advantage. Although widely discussed, this phenomenon has never been tested in a phylogenetic context. We reconstructed a mitochondrial DNA (mtDNA) tree to investigate the phylogenetic distribution of pond and lake lifestyles among 10 species of northern temperate Chaoborus midge larvae. The mtDNA tree is similar to previous morphological trees for Chaoborus, the only difference being the disruption of the subgenus Chaoborus sensu stricto. At least three shifts have occurred between pond and lake lifestyles, each time associated with evolution of diel vertical migration in the lake taxon. The trend in larval body size with habitat type is sensitive to tree and character reconstruction methods, only weakly consistent with the effects of fish predation. Despite long time periods over which adaptation to each habitat type could have occurred, there remains significant phylogenetic heritability in larval body size. The tree provides a framework for comparative studies of the metapopulation genetic consequences of pond and lake lifestyles.