Abstract: The genus Coelastrella was taxonomically positioned in the family Scenedesmaceae (Sphaeropleales, Chlorophyceae), and was characterized as unicellular or few-celled aggregations. Species within the genus are mostly found in aerial and sub-aerial habitats, which are different from other freshwater-living members of Scenedesmaceae. They have good tolerance to some stress conditions, such as high temperature, high salt, and ultraviolet. The most notable feature of the genus Coelastrella is that the cells tend to accumulate carotenoids and oils in the late growth stage, or under some stress conditions such as nitrogen deficiency and high salt. This group has been proved to have broad application prospects in the fields of natural antioxidants and food pigment production. In this study, two strains of the genus Coelastrella were collected from Chongqing and Xinyang, and they were identified as a new species of the genus Coelastrella by morphology and three molecular markers of 18S rDNA, ITS, and tufA gene. The remarkable morphological feature of Coelastrella chongqingensis is that the cell wall is approximately smooth or only slightly wrinkled, without the meridianal ribs of the typical Coelastrella species. The young cells are mostly ellipsoidal or oval with obtuse ends with a size of (0—9) μm×(5—7) μm. The mature cells are mostly spherical or ellipsoidal with a size of 8—14—(18) μm. The results of the phylogenetic analysis showed that Coelastrella chongqingensis was closely related to Coelastrella vacuolata and Coelastrella tenuitheca. They all have similar morphotype, and formed independent monophyletic group in the phylogeny of tufA gene. This branch represents the third morphotype of Coelastrella, that is, the cell wall is approximately smooth or with a network of fine ribs without the typical meridional ribs of Coelastrella.