An endemic diatom, Cyclotella rhomboideo-elliptica Skuja, from the Yunnan Plateau, has been disappearing gradually from some lakes of the plateau. This study investigated the diatom's distribution in 30 lakes and documents long-term population changes in the paleolimnological record of a deep lake, Lake Fuxian. Living cells of C. rhomboideo-elliptica were found in five Yunnan Plateau lakes in 1957, but cells were restricted to Lake Fuxian in 2005. Its absolute abundance fluctuated from low to high to low. Our study suggests that nutrient concentrations correlate with C. rhomboideo-elliptica's s abundance and survival. We infer that the disappearance of C. rhomboideo-elliptica in some lakes may be due to increased nutrient concentrations and the species may be indicators of low nutrients. During the study, we also found that decreased in the diatoms average long axis length after the early 1990s. This morphological change was likely due to higher nutrient concentrations or to the increase in temperature, or a combination of the two.