The upper reaches of the Yangtze River posses many endemic and rare species of fish. It is one of the key regions of biodiversity protection in China. Coreius guichenoti is an endemic species in the upper Yangtze River, and is a common migratory species between the lower and the upper reaches of the channel. In relatively recent years, the construction of large hydroelectric projects may have impeded the migratory route taken by C. guichenoti. This has led to concern about how the population dynamics of the species could be affected. In order to better understand the population abundance and distribution of C. guichenoti, investigations were performed on fishing and catch composition in Jiangjin and Yibin sections of the Yangtze River in 2007–2009. The annual yields were analyzed based on the catch per unit effort, and the stocks of C. guichenoti were assessed by length–structure Virtual Population Analysis in the software package of FiSAT. The results showed that the total annual yield in Jiangjin section in 2007, 2008 and 2009 was 267 850、689 975 and 586 575 individuals and that in Yibin section was 485 100, 108 075 and 169 950 individuals, respectively. The annual yield of C. guichenoti in Jiangjin section was 56 932, 98 323 and 100 620 individuals and that in Yibin section was 66 099, 16 952 and 32 812 individuals, respectively. The catch was dominated by individuals of 80~220mm in length. From 2007–2009 the evaluated annual abundance of C. guichenoti in Jiangjin section of the Yangtze River was 319 416, 905 715 and 1 124 470 individuals respectively, and the annual average value was 783 200 individuals. The annual weight was 25.33, 129.72 and 244.48 t. The average value over these three years was 133.18 t. The annual abundance of C. guichenoti in Yibin section over the same time period was 469 395, 191 207 and 200 197 individuals, and the annual average value was 286 933 individuals; the annual weight was 60.18, 43.11 and 15.14 t, and the annual average value was 39.48 t. It was concluded that the stock of C. guichenoti in Jiangjin section was much larger than that in Yibin section, and the stock showed a decreasing trend in Yibin section but an increasing trend in Jiangjin section during 2007–2009.