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There is increasing interest in the genetic diversity and phylogeography of aquatic invertebrate zooplankton in the Eastern Palearctic, yet these topics remain largely unexplored in China. Here, we investigated the lineage diversity and phylogeography of an important cladoceran taxon, the Chydorus sphaericus (Crustacea: Cladocera) species complex, which is common in various aquatic habitats. We found populations of this species complex in 30 of 154 waterbodies across China. Analysis of DNA sequences from a portion of the mitochondrial cytochrome c oxidase subunit I gene placed these populations in three lineages, one of them not previously recognized. There was a clear geographical separation of C. sphaericus lineages: lineage A2‐1 was the only lineage detected on the Qinghai‐Tibetan Plateau, whereas lineages A3‐1 and A3‐2 were present elsewhere in China. Several lineages (and even individual haplotypes) were widespread in Eurasia, suggesting an ability to disperse over long distances. Phylogenies based on nuclear ribosomal internal transcribed spacer fragments (both ITS‐1 and ITS‐2) recognized two distinct C. sphaericus clades in China. Interestingly, one specimen possessing mtDNA of lineage A3‐2 was found unexpectedly to have an ITS‐1 allele normally associated with mitochondrial lineage A2‐1, and ITS‐2 alleles consistent with this. This discordance between mtDNA and nuclear phylogenies is indicative of interspecific hybridization and gene introgression between different members of the species complex. This study contributes to an understanding of the genetic diversity of the C. sphaericus species complex in a Eurasian context. [ABSTRACT FROM AUTHOR]