Sampling was conducted on the Missouri and Yellowstone rivers, North Dakota to obtain information on the distribution, abundance and habitat use of the sturgeon chub (Macrhybopsis gelida) and sicklefin chub (M. meeki) (Family Cyprinidae), two declining benthic fish species native to the Missouri River basin. The study area consisted of three distinct river segments, the Missouri River near Williston, the Missouri River near Bismarck ( below Garrison Dam), and the Yellowstone River near its confluence with the Missouri River. Both species of chub were collected, mainly with a benthic trawl, throughout 94% of the range sampled in the Williston and Yellowstone segments. Sicklefin and sturgeon chubs were the second and third most abundant cyprinids, respectively, collected from the Williston and Yellowstone segments. Best-fit regression models indicated that the presence of sturgeon chubs increased with decreasing depth, increasing velocity and decreasing water clarity, and that the presence of sicklefin chubs increased with increasing depth, decreasing velocity and decreasing water clarity. In contrast, no chubs of either species were collected in trawls from the Bismarck segment. This segment had significantly deeper, faster, and clearer water than both the Williston and Yellowstone segments.