Rhinogobio ventralis, an endemic species in the upper Yangtze River, has been threatened by overfishing and dam construction. To understand its population dynamics after the Three Gorges Reservoir was built and before the Xiangjiaba and Xiluodu reservoirs were built, we employed body length-frequency data to estimate growth and mortality parameters, population abundance and utilization of the fish based on surveys in the Jiangjin and Yibin sections of the upper Yangtze River conducted from 2007-2009. Fish ranged from 52 to 250 mm in length and 2.7 to 307.2 g in weight, with an average length of 150.8 ± 40.7 mm and an average weight of 72.3 ± 49.7 g. The average size of the fish in the Jiangjin section of the Yangtze River (168.6 ± 29.5 mm) was significantly larger than that in Yibin section (125.6 ± 41.2 mm). The length-weight relationship of R. ventralis was well-fit with a power function, W = 6.06 × 10-6 L3.20 (R2 = 0.98, P < 0.01, n = 436). Asymptotic length (L∞) and growth constant (k) were estimated using length frequency data as 338 mm and 0.24/yr, respectively. Average natural mortality was comprehensively estimated as 0.43 using three empirical formulas proposed by Pauly, Gunderson & Dygert, and Jensen, respectively. The total mortalities were estimated using a length-converted catch curve analysis as 2.26 in the Jiangjin section and 2.09 in the Yibin section of the Yangtze River. The observed exploitation rates were 0.81 in the Jiangjin section and 0.79 in the Yibin section, which were higher than the maximum exploitation rates of 0.57 in the Jiangjin section and 0.62 in the Yibin section that were estimated using Beverton & Holt Y′/R analysis. Population abundance of R. ventralis in the Jiangjin section was estimated by length-structured virtual population analysis as 68,247 in 2007, 67,432 in 2008, and 176,266 in 2009, respectively, with an average of 103,982; while abundance in the Yibin section was estimated as 22,953 in 2007, 46,340 in 2008, and 34,021 in 2009, respectively, with an average of 34,438, indicating the population abundance was higher in the Jiangjin section than the Yibin section. We conclude that overfishing is occurring in these stocks of R. ventralis and recommend a longer period of monitoring in order to understand population dynamics of R. ventralis. We further suggest that management authorities establish a longer closed period for fishing and undertake habitat restoration to protect the endemic fish species.