Eutrophication and climate warming have intensified the global expansion of invasive cyanobacteria such as Cylindrospermopsis spp. and Chrysosporum spp. Cylindrospermopsin (CYN) produced by species of the latter two genera may harm phytoplankton, zooplankton, and fishes. However, effects of CYN on the bacterioplankton community have not been studied. Based on high-throughput sequencing, we explored the effect of CYN on the structure and function of the bacterioplankton community by adding pure CYN to in-situ water collected from a brackish coastal shallow lake: Dishui Lake, China. We found that most bacterioplankton taxa had a certain tolerance potential to CYN, but that high concentrations of CYN (40 mu g/L) caused a significant decrease in microbial abundance and functional groups. Of the dominant phyla, Actinobacteria had the strongest tolerance to CYN. Network analysis indicated that CYN caused shifts in the community structure of the bacterioplankton, reducing community stability and structural complexity. High CYN concentrations also reduced the correlation between the different bacterioplankton groups, and the abundances of some bacterial taxa associated with the denitrification function and the process of carbon transfer in the microbial food web were inhibited. Our study provides new insight into the response of the bacterioplankton communities to harmful algal toxins produced by cyanobacteria.