The Illinois River Biological Station monitors fish communities in the Illinois River using two different electrofishing programmes, one using three-phase alternating current [AC; The Long Term Illinois Fish Population Monitoring Program or long-term electrofishing (LTEF)] and the other pulsed direct current [DC; The Long Term Resource Monitoring Program (LTRMP)]. In 2001, we replicated three-phase AC sampling sites with pulsed-DC electrofishing gear to test for differences between the two collection methods and programmes. Electrofishing runs at each site were standardized by length and time, with 48 samples collected for each gear. Our objective was to test for differences in fish catch rates using total catch, species richness, fish size ranges, and sample composition and structure. Total catch was significantly greater for LTRMP electrofishing (4368 total fish, mean?=?91.0 fish per sample) compared with LTEF electrofishing (1423 total fish, mean?=?29.6 fish per sample). Species richness also was significantly greater for LTRMP electrofishing (50 total species, mean?=?12.9 species per site) compared with LTEF electrofishing (38 total species, mean?=?7.9 species per site). Size ranges of fishes, composed of 100-mm-length groups, showed higher total catches for the LTRMP within all length groups. Although our analyses suggest that collections from the LTRMP were significantly greater in most instances, a consistent pattern of species composition between the two programmes was not evident. Our results suggest that caution must be taken when attempting to compare fish community composition and structure information between these programmes. Copyright (c) 2011 John Wiley & Sons, Ltd.