AbstractThe effect of decomposition of Microcystis blooms on the sediment bacterial communities was investigated in a 14‐day mesocosm experiments under dark and anoxic condition with three differing levels of Microcystis spp. biomass (from 20 to 2000 µg L−1) as measured by chlorophyll‐a (Chl‐a) concentration in the water column. Sediment samples were collected on days 0 and 14 for bacterial community composition (BCC) analysis, based on rapid decreases in the Chl‐a concentration of water column. The BCC was determined by denaturing gradient gel electrophoresis and sequencing of predominant bands. The results showed that after Microcystis decomposition (day 14), the bacterial phylotype diversity in the sediment increased in enclosures with added Microcystis, and the relative abundance of bacteria affiliated with Bacteroidetes and Verrucomicrobia strongly increased. Canonical correspondence analysis showed that organic matter and Chl‐a contributed significantly to the changes in sediment bacterial communities during Microcystis decomposition. The present results demonstrate Microcystis decomposition may directly and indirectly influence the BCC of the sediment.