Thorea (Rhodophyta) is a genus of freshwater red algae whose species-level taxonomy has long been disputed because of poor sample representation and seemingly random distribution. Molecular evidence has recently led to the establishment of the new order Thoreales, but the phylogeny of the recognized species and their dispersal pattern have remained unclear. We analyzed most known Thorea samples, including two samples from Shanxi, China, based on sequences of two conserved genes—chloroplast rbcL and nuclear 18S rDNA. We reconstructed phylogenetic trees for Thorea and related taxa by Bayesian analysis, maximum likelihood, and maximum parsimony. Analyses of both genes consistently recovered a distinct clade including all Thorea samples. The Thorea clade was closely related to Nemalionopsis rather than to species in Batrachospermales, supporting the recognition of Thoreales. Two T. hispida samples from China formed a single clade most closely related to conspecific samples from Japan. In addition, T. okadae from Japan was sister to T. hispida, suggesting the former species may be synonymous with T. hispida rather than T. violacea. Analysis of geographic information mapped onto the rbcL tree indicated that Thorea originated in the Northern Hemisphere, most probably in Asia, despite the disjunction between Asia and North America.