Microbial community compositions and functions of freshwater ecosystems vary due to the environmental parameters and water chemistry. Transient bloom events play a crucial role on the community profiles. In this study, a specific focus was set to provide a snapshot of the bacterial community composition in Lake Sapanca, associated with cyanobacterial bloom by high throughput sequencing method. For this purpose, a sample was collected in the shore of Lake Sapanca during a cyanobacterial bloom, and the bacterial community profile was examined by 16S rRNA amplicon sequencing using the Illumina MiSeq platform. Cyanobacteria represented 94% of the all reads. The bacterial community was re-calculated to evaluate the bacterial diversity in detail by filtering cyanobacterial sequences. The community was dominated by Proteobacteria (44%) and Bacteroidetes (33%) species which are abundant in freshwater ecosystems having an ability to degrade complex organics. Among the classified genera, Flavobacterium and Rheinheimera dominated the bacterial community suggesting a strong link between those species and the cyanobacterial bloom. The experimental work presented here provides one of the first investigations of total bacterial communities in Lake Sapanca by the high throughput sequencing method. Further work is needed with more sampling points and time series to fully understand the bacterial diversity and dynamics.