In Lake Pontchartrain Basin, commercial fishing in estuarine habitats impacts many non-target species collected as bycatch. I investigated the bycatch assemblages collected by commercial vessels and compared these to assemblages collected by typical fishery-independent methods. I compared assemblages using analysis of similarity (ANOSIM) and determined important species by weight and abundance using similarity percentages analyses (SIMPER). I also examined differences in size-class distributions by gear type using density kernel plots and Mann-Whitney U tests. The two gear types collected significantly different assemblages (ANOSIM R = 0.522, p = 0.001) and gear type explained more composition differences than other factors such as month, daytime, or location. Fishery-independent gear underestimated the importance of many species. Although fishery-independent data are invaluable for monitoring assemblage dynamics, fishery-independent gear collects different assemblages than commercial gear. Larger fishes of important species were caught less often in bycatch, but completely absent from fishery-independent gear.