New York State's fauna is exceptionally rich in odonates (dragonflies and damselflies), whose lengthy aquatic larval phases render them susceptible to effects of lake acidification, including the loss of fish. We used a collection of benthic macroinvertebrate samples taken by the Adirondack Lakes Survey Corporation to compare odonate communities in 460 lakes. Half were from the Adirondack Mountains, where acid neutralizing capacity (ANC) is low (mean ANC = 108.0 μg/L) and Al concentrations are high (mean Al = 111.61 μg/L), and half were from the Lower Hudson Valley, where ANC is significantly higher (mean ANC = 554.6 μg/L) and Al is significantly lower (mean Al = 0.049 μg/L). Many more lakes in the Adirondack lakes were fishless (52) compared to the lower Hudson (3), and the pH in Adirondack fishless lakes was an order of magnitude lower than the pH of Adirondack lakes with fish. Ninety-nine odonate taxa were identified (86 to species). In Adirondack samples, co-occurrence patterns were correlated with presence or absence of insectivorous fish and with acidic waters. Similar patterns were not apparent in Lower Hudson Valley samples. In Adirondack samples, richness of common taxa (found in ≥20 lakes) was higher in lakes with fish than in lakes without fish, regardless of pH. Loss of fish may enhance the top predator role of large larval dragonflies, causing change in odonate community structure, an interpretation consistent with previous research. Acidification of Adirondack lakes appears to promote a nonrandom subset of possible odonate communities, with negative implications for regional diversity.