Abstract: Protoperidinium is one of the most species-diverse genera of marine dinoflagellates. As a group of heterotrophic plankton, it plays important ecological roles in marine food webs. However, species of this genus are morphologically complex and often difficult to identify, and the long-term lack of a regionally applicable taxonomic key for Chinese seawaters has constrained studies on local species diversity. Using all species of Protoperidinium recorded in Dinoflagellates in the China's Seas Ⅲ (Peridiniales) as the study material, we systematically extracted 32 morphological characters belonging to seven categories: apical horns and antapical appendages, ventral view, sulcus, cingulum, thecal plate pattern, thecal ornamentation, and cell size. These characters were comprehensively evaluated in terms of intraspecific stability, interspecific discriminability, and ease of observation under light microscopy. The apical horns and antapical appendages, sulcus, and ventral view were identified as the core diagnostic characters, whereas the remaining characters were treated as supplementary evidence. On this basis, a dichotomous taxonomic key was constructed and subsequently evaluated for practical applicability. Four professional taxonomists achieved identification success rates of 90.0%−93.3% when using randomly grouped species illustrations. This is the first localized morphological taxonomic key covering 118 Protoperidinium species (Including varieties) in Chinese seawaters, with a trinity cross-verification mechanism of “key-illustration-description”. The key has been applied efficiently and reliably in marine ecological monitoring in Guangdong Province, providing solid taxonomic support for enhancing phytoplankton monitoring capacity in the South China Sea.