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Background  China is an important biogeographical zone in which the genetic legacies of the Tertiary and Quaternary periods are abundant, and the contemporary geography environment plays an important role in species distribution. Therefore, many biogeographical studies have focused on the organisms of the region, especially zooplankton, which is essential in the formation of biogeographical principles. Moreover, the generality of endemism also reinforces the need for detailed regional studies of zooplankton.  Bosmina , a group of cosmopolitan zooplankton, is difficult to identify by morphology, and no genetic data are available to date to assess this species complex in China. In this study, 48 waterbodies were sampled covering a large geographical and ecological range in China, the goal of this research is to explore the species distribution of  Bosmina  across China and to reveal the genetic information of this species complex, based on two genetic markers (a mtDNA 16S and a nuclear ITS). The diversity of taxa in the  Bosmina  across China was investigated using molecular tools for the first time.    Results  Two main species were detected in 35 waterbodies: an endemic east Asia  B. fatalis , and the  B. longirostris  that has a Holarctic distribution.  B. fatalis  had lower genetic polymorphism and population differentiation than  B. longirostris. B. fatalis  was preponderant in central and eastern China, whereas  B. longirostris  was dominated in western China. The third lineage ( B. hagmanni ) was only detected in a reservoir (CJR) of eastern China (Guangdong province).  Bosmina  had limited distribution on the Tibetan plateau.    Conclusions  This study revealed that the biogeography of  Bosmina  appear to be affected by historical events (Pleistocene glaciations) and contemporary environment (such as altitude, eutrophication and isolated habitat).    Electronic supplementary material  The online version of this article (10.1186/s12862-019-1474-4) contains supplementary material, which is available to authorized users.

Diversity of the Bosmina (Cladocera: Bosminidae) in China, revealed by analysis of two genetic markers (mtDNA 16S and a nuclear ITS)