The reproductive biology of three yellow catfish congeners was studied in the Three Gorges Reservoir of the Yangtze River, China. We compared reproductive traits among the lentic, transitional, and lotic zones. A total of 4502 individuals of the three species was collected, and the sex ratio, size at 50% maturity, spawning season, fecundity, and egg size were determined. Results showed that populations inhabiting the lotic zone spawned earlier than those inhabiting the lentic zone. For the three species, fecundities were significantly higher for populations in the lotic zone than for those in the lentic and transitional zones (P < 0.05). Pelteobagrus vachelli (Richardson) and P. fulvidraco (Richardson) displayed an obvious trade-off between egg size and fecundity, whereas P. nitidus (Sauvage et Dabry) produced the largest eggs in the lotic zone. Sex ratios were significantly different among zones (P < 0.05, for each species), but the bias patterns were different. Sizes at 50% maturity of female P. nitidus and P. vachelli were the largest in the lotic zone and the smallest in the transitional zone, but was similar among zones for P. fulvidraco. Overall results suggest that the three yellow catfish species developed different reproductive traits among the three habitats in the TGR, whereas the variations reflected further interspecific differences. Our study indicates the importance of riverine habitats for the conservation of species of fish, even for species such as these eurytopic catfish inhabiting the upper reach of the Yangtze River. This study further suggests that species-specific responses should be considered when evaluating the influences of new hydropower projects, even for such closely related species of fish.