Information on the distribution and abundance of rare fishes is critical for permitting, consulting, and conservation planning. However, great-large river monitoring programs target sportfish or the whole assemblage, providing limited data on small-bodied Species of Greatest Conservation Need (SGCN), including the state and federally listed. This data gap compromises effective SGCN monitoring. To address this challenge, we assessed six sampling gears for detecting the 19 SGCNs recorded in the Mississippi River (MR) and Wabash River (WR) and characterizing fish assemblage. Replicate samples were collected at 15 MR and 10 WR sites with backpack electrofishing, boat electrofishing, benthic trawling, cast netting, minnow traps, and seining. The number of fish species and individuals were counted for each type of gear at each site. Boat electrofishing (BE) is most productive, contributing on average 49% and 34% of all species captured at each site. Trawling is highly complementary to BE, capturing most SGCN species and individuals, although it only contributed on average 18% of all species at a site in WR, 6% in MR. These two gears combined detected all 6 SGCN. In a 2D-NMDS plot, samples from each river are grouped largely based on gear type, particularly BE and trawling, instead of sites, indicating poor sample comparability among the different gears. We conclude that trawling is the most effective to capture SGCN while BE is the most effective to characterize the whole fish assemblage in the great-large rivers in Illinois. Joint use of two methods would meet most monitoring needs for biodiversity conservation.