The combination of low pH and high concentrations of metals associated with acid mine drainage would have severe toxicological effects on aquatic ecosystems. In order to evaluate the potential impact of acid mine drainage on the benthic algal communities in Gaolan River, which is one of the three main tributaries of Xiangxi River, we chose three sites in pyrite mining area as impaired group (I), four uninfluenced sites were taken as control group (C) and five sites as recovery group (R). The results showed that benthic algal density, chlorophyll a concentration, ash free dry mass (AFDM) and autotrophic index (AI) were significantly affected by acid mine drainage from pyrite in the upstream of Gaolan River, while dry season affected seriously than flood season. Correlation analysis showed autotrophic index was positively correlated with metals and negatively correlated with pH, so AI could be a better indicator in the case where a pollutant such as acid mine drainages.