Twelve putative “Chantransia” isolates were collected from six locations across Hubei, Shanxi, Guizhou, and Henan Provinces in China. Their morphological characters were evaluated via the Ward's method of hierarchical cluster analysis in SPSS software to classify phylogenetic relationships among the isolates. The morphological data revealed that isolate HN31 (called group “MALL”) was distinct from the other specimens being macroscopic with large vegetative cells and monosporangia (>20 μm in diameter). The 11 other isolates were grouped into three clusters, corresponding to the species Audouinella tenella , A . hermannii , and A . pygmaea . The morphological “Chantransia” stage of the species, reportedly belonging to the orders Batrachospermales, Thoreales, and the phylogenetically distant genus Audouinella , are very similar, resulting in the difficulty to distinguish them based just on morphology. Therefore, molecular analysis of rbc L, UPA, and COI-5P was conducted to infer the phylogenetic position of all isolates in this study. All “ A . tenella ” and “ A . hermannii ” sequences belong to order Batrachospermales, while the isolate HN31 was the “Chantransia” of Thorea hispida . The six other specimens varied morphologically, but they were within the circumscription of “ A . pygmaea ”. All three molecular markers show that all “ pygmaea ” isolates also represent the “Chantransia” of T . hispida . Furthermore, results from this investigation proposed a new species— Sheathia qinyuanensis , corresponding to the isolates QY1 and QY2.