Bosmina is a globally distributed zooplankton that adapts to a eutrophic environment. In this study, we cultivated monoclonal Bosmina fatalis and determined its complete mitochondrial gene sequence using the Illumina HiSeq 4000 platform. It was 15,209 bp in length, including 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes, with the A + T content (69.2%) significantly higher than the G + C content (30.9%). All 22 typical tRNA genes had a classical cloverleaf structure, except for tRNAIle. The complete mitochondrial genome of nine other cladoceran species was used to reconstruct a phylogenetic tree, showing that B. fatalis has a closer relationship with Daphnia than other cladocerans., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)