Dam cascades have been a major threat to fishes of the upper Yangtze River. The remaining lotic river segment of the upper mainstem between the Xiangjiaba Dam (XJD) and the Three Gorges Reservoir (TGR) may serve as a critical refuge for endemic fishes. We investigated distribution of ichthyoplankton Botia superciliaris, an endemic species, at three sections preimpoundment and postimpoundment of the XJD, that is, Yibin (close to the XJD), Zhuyang (in the middle of the segment), and Mudong (in the tail of the TGR). Preimpoundment of the XJD, larvae occurred in all three sections, and their abundance tended to be highest at Yibin and lowest at Mudong. Postimpoundment, larval abundance dramatically decreased in all three sections. In particular, no larvae were found at Yibin, and larval abundance tended to be higher at Zhuyang than at Mudong. Eggs were collected from all three sections, and those from Zhuyang accounted for over 90% of the total. Initiation of egg occurrence at Yibin was approximately 1 month later than at Zhuyang and Mudong. Water temperature was lower, and water transparency was higher at Yibin than at Zhuyang and Mudong postimpoundment. We suggest that the decrease in abundance and delayed presence of ichthyoplankton at Yibin postimpoundment of the XJD reflected the impact of upstream dam discharge and that the lower abundance of ichthyoplankton at Mudong compared with Zhuyang both preimpoundment and postimpoundment of the XJD reflected the influence of inundation by the TGR. We recommend that the river sections around Zhuyang become high-priority conservation areas