In order to understand the phylogeny of Rotaria sordida in China and the world, and to clarify the driving factors of the genetic differentiation of bdelloid rotifers, R. sordida samples were collected from 12 cities in 10 provinces of China, and 32 COⅠ gene sequences were obtained. Moreover, 47 COⅠ gene sequences from Europe and Oceania in the GenBank database were downloaded, and the Bayesian phylogenetic tree was constructed at China and global scales, respectively. The results showed that the COⅠ gene sequences of R. sordida in China were divided into two taxonomic clusters, and their phylogenetic relationships were not only affected by geographical location, but also related to habitat types. At global level, all sequences were also divided into two clusters, and some sequences in China were clustered with sequences from Europe and Oceania. The bdelloids with the same habitat type in the two clusters had high homology. It was speculated that the phylogeny of bdelloid rotifers was driven by geographic distribution and habitat heterogeneity. Genetic diversity analysis based on the Generalized Mixed Yule Coalescent model (GMYC) showed that 22 haplotypes and 12 cryptic species were identified from the COⅠ sequence of R. sordida in China; 45 haplotypes and 28 cryptic species were identified from the global COⅠ sequence. This indicated the high hidden diversity in R. sordida species complexes. Therefore, habitat heterogeneity played an important role in cryptic species differentiation of R. sordida. This study preliminarily explained the phylogenetic relationship and genetic diversity of R. sordida in China and the world. Furthermore, this study supplemented the COⅠ gene database of bdelloid rotifers in China, and provided basic data for lineage biogeographic studies in the future.