The Caspian Sea is one of the most polluted seas in the world due to industrial and agricultural effluents as well as extraction of oil and gas reserves. Microbial communities can impact the fate of contaminants and nutrients. However, insight into the microbial ecology of the Caspian Sea significantly lags behind other marine systems. Here we describe the microbial diversity of sediments collected from three sampling stations in the Caspian Sea. This study provides a baseline assessment that may serve as a point of reference as this system changes or as remediation efforts are initiated to reduce pollution.