Abstract: Green euglenoids are a freshwater group with photosynthetic autotrophic ability in the phylum Euglenophyta, with over 1000species reported globally. They possess both ecological indicator value (as typical indicator organisms for eutrophic water bodies) and economic value (with high-protein and high-nutrition characteristics, and are widely used in food, feed, and fertilizers). Before the 20th century, their classification mainly relied on classic morphological indicators. However, the morphological similarity of single-celled algae and the unique euglenoid movement made species identification difficult, leading to frequent duplicate reports of the same species and considerable confusion in the classification system. Since the 21st century, phylogenetic studies based on molecular markers have promoted the reconstruction of the classification system. Molecular evidence clearly shows that green euglenoids form a monophyletic group. Due to the polyphyly issue, the genus Euglena has been split into new taxonomic units, whereas the genera Phacus and Lepocinclis have been established as the family Phacaceae. However, the introduction of molecular data has also ledto a disconnection between morphology and phylogenetic results. For important groups such as Trachelomonas and Strombomonas, although molecular studies support their independence, data coverage remains extremely low (molecular data exist for only 25species of Trachelomonas and 10species). The lack of morphological transitional species further hinders the analysis of phylogenetic relationships. The morphological definition of Lepocinclis has become blurred due to the transfer of Euglena species, and the iconic characteristic of cell flattening in Phacus has been broken due to the addition of non-flattened species. Recent breakthroughs in omics technologies have filled long-standing data gaps across multiple key evolutionary lineages of this clade. Accumulated evidence from existing studies has confirmed that green euglenoid chloroplasts trace their origin to a single secondary endosymbiotic event involving green algae, resolved the evolutionary trajectories of organelle genomes within this clade, and provided whole-genome level validation for the shopping bag hypothesis, which posits multiple independent plastid acquisitions by the ancestor of green euglenoids. Furthermore, the first high-quality, chromosome-level de novo genome assembly of euglenoids has recently been completed, breaking the long-standing technical bottleneck that has historically hampered progress in this field. Collectively, these advances establish an unprecedented molecular foundation for the taxonomic delimitation and evolutionary history reconstruction of green euglenoids. Research on green euglenoids in China began with the first report by Wang Jiaji in 1925. In 1999, the Flora Algarum Sinicarum Aquae Dulcis systematically recorded 9 genera and 318species. In recent years, one new species of Trachelomonas and 9 newly recorded species of Euglena in China have been reported by combining morphological and molecular methods, providing basic data for biogeographical research. Future research should integrate morphological and molecular biological methods, establish a classification standard that takes into account both morphological distinguishability and genetic consistency, expand the sampling scope to improve the representativeness of phylogenetic analysis, and leverage the advantages of China's freshwater ecosystem to support further studies. The unique mesokaryotic structure, three-membrane chloroplasts, and non-simplified genome characteristics of green euglenoids serve as a key model for the study of eukaryotic evolution.