Abstract: Euglenaria Karnkowska, Linton & Kwiatowski is a new genus isolated from Euglena Ehrenberg in 2010. Currently, there are 4 species reported in the world. In China’s existing algal taxonomic data, the species of Euglenaria are still classified in Euglena, and their morphological description is vague, making it difficult to distinguish them from some species of Euglena. It is difficult to identify Euglenaria and Euglena, and there is no obvious difference between Euglenaria and some species of Euglena in morphology. With the development of molecular biology, new technical means have been brought for the identification of euglenoid. While further research on the systematic classification of euglenoid has been carried out, the classification status of many euglenoid species has been revised, and Euglenaria is a new genus separated from Euglena at this stage. Our study found that the cells of Euglenaria are generally fusiform without mucocysts, and the Chloroplasts are disc-shaped with pyrenoids and edges irregular with deep grooves. The morphological differences among the species of Euglenaria are mainly reflected in the shape, number of chloroplasts and size of cells. The cells morphology of Eu. clepsydroides are hourglass shaped. The cells of Eu. caudata length (58.95±12.38) μm, width (28.57±5.82) μm were the largest. The chloroplast number of Eu. anabaena and Eu. clavata was significantly different. Eu. anabaena contained fewer chloroplasts (only 4±1), while Eu. clavata cells contained 10±3 chloroplasts. The morphological differences among species of Euglenaria are very subtle, and it is difficult to correctly identify them. The phylogenetic tree showed that with the closely related Eutreptiaceae as the outgroup, the results indicated that the rest of the euglenoids were divided into two major clades, the Euglenaceae clade and the Phacaceae clade. Euglenaceae (0.96/597) included Euglenaformis, Strombomonas, Trachelomonas, Cryptoglena, Euglena, Monomorphina, Euglenaria and Colacium. Each genus formed a well-supported evolutionary clade, respectively. The genus Euglenaria is located in the branch of Euglenaceae (0.84/-), consisting 28 strains of Euglenaria, which are divided into 3 subbranches, and the support rate of each subbranch exceed 99%. Eu1 clade contained 13 strains of Eu. anabaena, Eu2 (1.00/998) contained 8 strains Eu. caudata, and Eu3 (1.00/1000) contained 6 strains Eu. clavata. Eu. anabaena and Eu. caudata were sister branches. However, there are great difference in cell size and chloroplast number between the two species. In morphology, Eu. anabaena and Eu. clavata were more similar, with similar cell size and large difference in chloroplast number. There were significant differences in cell size between Eu. caudata and Eu. clavata, but the number of chloroplasts was similar. This suggests that the relationship between morphology and molecular phylogeny may be inconsistent. At present, there are only 4 species of Euglenaria and 162 species of Euglena, and 80% species of Euglena have no molecular data. It is unknown whether there are still Euglena species belonging to Euglenaria among these species without molecular data, and further research is still needed. In this study, 12 strains of Euglenaria collected from China were used as materials to study the phylogeny of Euglenaria based on morphological and molecular biological methods. We provide the Euglenaria species in morphological characters and molecular data and discusse the phylogenetic position of Euglenaria. In order to improve the taxonomic description of this group in China, we revised the taxonomic description of Euglenaria.