Cladocerans of the Daphnia longispina complex are often the key components of pelagic food webs in northern temperate lakes and ponds. In the present study, we aimed to fill the gap in knowledge on the biogeography and diversity of this species complex, through analysis (by sequencing two mitochondrial genes) of the taxonomic structure of 18 lake populations across China, covering a large geographical and ecological range. Based on the patterns observed in the Western Palaearctic and Japan, we hypothesized that several species of the D. longispina complex should coexist and that some cryptic lineages are present in China. In the lakes studied, however, we detected haplotypes of only two species (D. galeata and D. dentifera). Daphnia galeata was detected in eutrophic lakes at lower altitudes (in central and eastern China), whereas D. dentifera was found in high-altitude oligotrophic lakes of the Tibetan Plateau in western China. The two lineages coexisted in only one of the lakes studied, in Tibet. The variation in mitochondrial DNA differed between the two species. Daphnia dentifera haplotypes were lake specific, while D. galeata haplotypes were often shared across lakes and geographic regions, indicating a recent rapid expansion of the latter species.