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In 1997 and 1998, we sampled the Missouri River, North Dakota to determine if anthropogenic disturbances had influenced catostomid species composition and feeding ecology. We compared two distinct river segments, the Missouri River between the mouth of the Yellowstone River and Lake Sakakawea (the Yellowstone–Sakakawea segment (YSS)), a moderately altered segment and the Missouri River between Garrison Dam and Lake Oahe (the Garrison–Oahe segment (GOS)), a highly altered segment. The segments exhibited greatly different sucker communities. Bigmouth buffalo, Ictiobus cyprinellus, smallmouth buffalo, Ictiobus bubalus, and river carpsucker, Carpiodes carpio, represented 94% of the sucker catch in the YSS, whereas in the GOS, white sucker, Catostomus commersoni, and longnose sucker, Catostomus catostomus, constituted 98% of the sucker catch. In the YSS, high zooplankton densities led to greater sucker zooplanktivory and food niche overlap than in the GOS. Intense anthropogenic disturbances to the GOS are associated with the differences in sucker species composition, prey density and composition, and sucker feeding ecology between the two segments.