The environmental impacts and risks of nanomaterials that are commonly used in different technologies are of great concern as their toxic effects on the aquatic ecosystem remain unclear. In this study, bismuth sulfide (Bi2S3) nanoflowers (nfs) were synthesized using a microwave-based hydrothermal process, and their genotoxic effects were investigated in the common carp, Cyprinus carpio. Bi2S3 nanoflowers were applied to common carp for 96 h. LC50 value (LC50 = 350 mg/L−1) was determined for acute toxicity with probit analysis, and three sublethal concentrations (35, 87, and 175 mg/L−1) were selected accordingly for genotoxicity tests. Such LC50 value − 350 mg L−1 for the common carp makes these nanoflowers non-toxic to aquatic organisms according to the EU-Directive 93/67/EEC classification scheme. Toxicological evaluations of the sublethal concentrations of Bi2S3 nanoflowers demonstrated that the 35 and 87 mg L−1 Bi2S3nfs groups were generally harmless and similar to the control group. Only the 175 mg L−1 Bi2S3nfs group had significant DNA damage frequency and nuclear abnormalities than the control and other Bi2S3nfs groups. To the best of our knowledge, this is a novel data on genotoxicity reported for fish species exposed to Bi2S3 nanoflowers; however, further systematic studies need to be performed to fully estimate the effects of Bi2S3 nanoflowers on aquatic life.