Genetic differentiations and phylogeographical patterns of small organisms may be shaped by spatial isolation, environmental gradients and gene flow. However, knowledge about genetic differentiation of rotifers on intercontinental gradient is still limited. Polyarthra dolichoptera and P. vulgaris are cosmopolitan rotifers and tolerant to environmental changes, offering an excellent model to address the research gap. Here, we investigated the populations in Southern China and eastern North America, and evaluated the phylogeographical patterns from their geographical range sizes, geographic-genetic distance relationships and their response to spatial-environmental factors. Using mitichondrial cytochrome c oxidase subunit I gene as the DNA marker, we analyzed a total of 170 individuals. At least 24 putative cryptic species, including 20 of P. dolichoptera and 4 of P. vulgaris were detected based on three delimitation methods. Our results showed that some cryptic species were widely distributed but most of them were limited to single areas. The divergence of P. dolichoptera and P. vulgaris complexes indicated that gene flow between continents was limited while that within each continent was stronger. Furthermore, on the intercontinental scale spatial distance had a stronger influence than physicochemical variables on the genetic differentiations of P. dolichoptera and P. vulgaris complexes. However, the relationship between genetic distance and geographic distance was not continuously linear and the P. dolichoptera data best fitted the power-law model. This might be due to the effects of habitat heterogeneity, long-distance colonization and oceanographic barriers. Outliers above the correlation line between geographic distance and genetic distance suggest a significant dispersal barrier on large geographic scales studies.