Spatial and temporal variation of fish assemblages were investigated seasonally from May 2007 to February 2008across 11 study sites in a subtropical small stream, the Puxi Stream, of the Huangshan Mountain. Along the longitudinal gradientfrom headwater to downstream, fish species richness and abundance increased gradually, but then decreased significantly at thelower reaches. The highest species richness and abundance were observed in August and the lowest in February. Based on analysisof similarities (ANOSIM), fish assemblages were significantly different in spatial variation but not in temporal variation. Althoughdifferences were observed both among sites and among stream orders, the lower R value in order-variation suggestedstream order was not the optimal factor explaining the spatial variation of fish assemblages. In addition, dam construction did notsignificantly alter fish assemblages in the sites adjacent to and immediately downstream to dams. Using cluster analysis andnon-metric Multi Dimensional Scaling analysis (NMS), assemblages were separated into three groups at a Bray-Curtis similarityvalue of 42%: the upper, middle and lower groups. Following analysis of similarity percentages of species contributions (SIMPER),shifts in occurrence or abundance of S. curriculus, Z. platypus, R. bitterling and A.fasciatus contributed most to the differencesamongst the three groups. Standard Deviation Redundancy Analysis (RDA) suggested that habitat structure (such as elevation,substrate, and flow velocity) contributed to the spatial and temporal pattern of fish assemblages in the Puxi Stream. In conclusion,the fish assemblages in Puxi Stream presented significant spatial but not temporal variation. Human disturbance has perhapsinduced the decrease in species diversity in the lower reaches. However, no significant change was observed for fish assemblagesin sites far from and immediately downstream from low-head dams