Based on the data collected from the Suichuan and Shushui Rivers, both tributaries of the Ganjiang River between April and July of 2015, the fish species identified were classified into 68 and 46 species, 14 and 12 families in the Suichuan River and Shushui River respectively. Cyprinidae is the most common family that accounts for 52.9% and 58.7% in the total number of fish species in the Suichuan River and Shushui River, respectively. The dominant species were Pseudohemiculter dispar, Squalidus argentatus, Silurus asotus and Leptobotia elongate for the Suichuan River and Squalidus argentatus, Acrossocheilus parallens, Pseudohemiculter dispar, Silurus asotus, Pelteobagrus fulvidraco, Acrossocheilus fasciatus and Zacco platypus for the Shushui River. The diversity of fish species showed more abundant and diverse for the Suichuan River. The composition of ecotype of fish indicated the rich diversities of ecotype in both the Suichuan and Shushui Rivers. The tributary (Suichuan River) and main stream of the Ganjiang River demonstrated a highly fauna similarity and the fish resources indicated its significance to maintain the fish diversity in the middle of the Ganjiang River and its benefits to the existence of the fish species in mountain streams. Dam construction, sand excavation and heavy metal pollution are the most significant threat to fish diversity and ecosystem functioning in Ganjiang River basin. In order to protect fish diversity and fisheries more effectively, relevant laws should be strengthened and conservation areas should be established for the survival of freshwater fish species.