In order to determine the relationship between stream habitat and fish assemblages, an investigation of fish assemblages and environmental variables in different habitat types was carried out in the headwater stream section of Lijiang River, China, from September to November 2016. In total, 2968 individuals belonging to 4 orders, 11 families, 26 genera and 37 species were collected. Cypriniformes emerged as the most species-rich order, accounting for 62.2% of the total species. The dominant species were Pseudogastromyzon fangi
, Zacco platypus
, Acrossocheilus parallens
and Erromyzon sinensis
. Non-metric multidimensional scaling (NMDS) and permutational multivariate analysis of variance (PERMANOVA) revealed that fish assemblages were not affected by habitat type. However, one-way ANOVA results showed that species richness, fish abundance, fish density and Shannon index were significantly affected by habitat type. Redundancy analysis (RDA) further revealed that altitude, velocity, conductivity, turbidity, depth and wetted width had significant relationships within fish assemblages, whereas water temperature, dissolved oxygen and substrate size were less important in this study, and different fish species preferred different environmental variables potentially due to differences in species’ ecological requirements. Although habitat type did not affect overall fish assemblages, habitat heterogeneity played an important role in fish diversity. Hence, maintaining diverse stream habitats or restoring them are of key importance for fish diversity conservation and sustainability management of rivers.
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