The Ausable and Boquet rivers are two of New York's major tributaries to Lake Champlain. The two watersheds are referred to as the Boquet/Ausable Subbasin. The Subbasin receives drainage from 795 square miles including diverse wetland types. From 2005 to 2009, a total of 768 sampling sites (324 in the Ausable watershed and 444 in the Boquet watershed) within 56 wetlands were surveyed from mid-June to mid-August. A total of 470 plant species were recorded, including 138 species of woody plants, 85 species of graminoids, 23 species of pteridophytes, and 224 herbaceous species. Included in the sampled plant species were 50 exotic species, 14 non-native invasive species, 2 New York State (NYS) endangered species, 2 threatened species, and 31 species listed as exploitably vulnerable by the New York State Natural Heritage Program. Herbaceous plants were the most abundant group and accounted for 48% of all species (45% at Ausable, 49% at Boquet). The least abundant group was the pteridophytes (5%). The Ausable watershed samples included a larger number of plant species (368) than the Boquet watershed samples (332). This difference was statistically significant (P = 0.001). The Ausable watershed had larger numbers of native, exotic, invasive, and vulnerable species than the Boquet watershed. The differences were statistically significant for the native plants (P < 0.001), exotic plants (P = 0.001), and exploitably vulnerable plant species (P = 0.005) observed in the two watersheds. However, the difference in non-native invasive plant species observed in the two watersheds was not statistically significant (P = 0.505). Plant species differences between the two watersheds might have resulted from variations of multiple environmental factors including elevation, soil types, water chemistry, nutrient levels, and anthropogenic factors.