To date, productivity–diversity relationships (PDR) in terrestrial ecosystems have predominantly been examined across large spatial scales, while freshwater ecosystem studies typically focus on short-term field surveys. Here sediment records are used to examine the long-term patterns of PDR from two large lakes, Fuxian and Dianchi, which are currently oligo-mesotrophic and hyper-eutrophic, respectively. Changes in lake productivity and community structure were reconstructed based on sedimentary pigment concentrations (i.e. Chl-a) and diatom assemblages. Principal Component Analysis (PCA) of diatom community data showed that primary productivity was the most significant environmental gradient driving diatom community changes in both lakes. Lake productivity was positively correlated to diatom alphaand beta-diversity indices in Lake Fuxian but negative in Lake Dianchi. The relationship between the magnitude of productivity change and diatom beta-diversity was significantly negative in Lake Dianchi while no trend was found in Lake Fuxian. There was a significantly negative relationship between diatom species richness and community productivity in Lake Dianchi, suggesting the influence of increased species richness in enhancing community productivity was overridden by human disturbances. Disturbance associated changes in limnological properties 90 生 物 多 样 性 Biodiversity Science 第 23卷 not only caused the loss of biodiversity, but also directly promoted diatom production through intensive nutrient enrichment.