The extant Chaoborus assemblage can be assessed using subfossil mandibles

1. Assemblages of Chaoborus were examined in 80 thermally stratified southern central Canadian Shield lakes to explore whether subfossil mandibles could be useful in assemblage‐level studies of Chaoborus. 2. Chaoborus (Sayomyia) (probably Chaoborus punctipennis in this study region) and Chaoborus flavicans were the most common taxa recorded, while Chaoborus trivittatus was rarer. Chaoborus americanus was not recorded in subfossil assemblages, because no fishless lakes were included in this study. Chaoborus flavicans had higher relative abundances (%) in lakes with higher dissolved organic carbon (DOC), probably because of reduced fish predation in less transparent water. 3. Results from logistic regression indicate that patterns of presence/absence for Chaoborus mandibles in the study lakes were influenced primarily by hypolimnetic oxygen concentration, probably because of the presence or extent of a hypolimnetic refugium from fish predation. 4. Chaoborus species richness in lakes, derived from subfossil assemblages, did not differ significantly from species richness estimates derived from plankton sampling with a net. Patterns of dominance and coexistence [e.g. the widespread co‐occurrence of C. flavicans and C. (Sayomyia)] determined from subfossil assemblages agreed with previous studies of the contemporary living assemblage. 5. These results suggest that subfossil assemblages may be used as an alternative to nocturnal plankton sampling to carry out research on the community ecology of Chaoborus. 6. We propose a hierarchical conceptual model of assemblage‐level patterns of Chaoborus in temperate lakes. Chaoborus americanus dominates in fishless lakes, whereas in lakes with fish Chaoborus is typically absent where there is no anoxic hyplimnion. In lakes with anoxic strata, C. trivittatus tends to dominate in lakes with few fish; in the remaining lakes, C. flavicans and C. (Sayomyia) dominate, although C. flavicans is more relatively abundant in lakes with lower water clarity (higher DOC).