Biological control is considered the best management option against the aquatic weed Hydrilla verticillata, one of the most damaging invasive plants in the United States. The search for natural enemies is ongoing. Larval flies from two families (Ephydridae and Chironomidae) were collected feeding on H. verticillata during recent surveys across China and Korea (the possible origin of both the monoecious and dioecious forms of this weed found in the United States). DNA barcoding was used to provide initial identifications, using the Barcode of Life database. In addition, we assessed the genetic structuring and geographic distribution of each provisionally identified species. Four distinct Hydrellia (Ephydridae) clades were identified. The species identity of these clades could not be confirmed, although two form part of the Hydrellia pakistanae species group. Significant genetic structuring was observed within the most widespread clade, suggesting it may comprise several species, although further investigation is required. Fourteen distinct chironomid clades were identified, nine of which correspond to previously described species. Genetic diversity within the chironomid species was low, even across a broad spatial scale, though some genetic structuring was observed in Cricotopus sylvestris. The results of this study provide direction for additional sampling of H. verticillata across China and Korea. Specifically, we recommend further surveys in Zhouzhuang (China), Yeonpori, Yangsancheon, and Deokeuwonri (all Korea). These surveys should be complemented with structured population genetics screening of both plant and insect material; this will help resolve the species status and host associations of the discrete mitochondrial lineages identified in this study.