(1) Background: The identification of Tropidothorax cruciger and T. sinensis is often complicated by the presence of the “intermediate form”. Due to the lack of molecular data, the taxonomic status of the “intermediate form” and the species boundaries between T. cruciger and T. sinensis remain uncertain; (2) Methods: In this study, we integrated morphological, molecular, and ecological data to delimit species boundaries of these two species using multiple species delimitation approaches; (3) Results: Most species delimitation analyses based on the cytochrome c oxidase subunit I (COI) fragment suggested that T. cruciger and the “intermediate form” comprised a single species, with T. sinensis representing a separate species. This delimitation result was also supported by the analyses of BFD* and genetic clustering based on genome-wide SNPs. Under this species delimitation scenario, a clear-cut barcode gap was discovered between the interspecific and intraspecific genetic distances. In addition, environmental-related analyses showed highly similar ecological requirements of T. cruciger and the “intermediate form”, supporting their recognition as a single species; (4) Conclusions: This study clarifies the taxonomic status of the “intermediate form” and the species boundaries between T. cruciger and T. sinensis, which is essential for further studies of ecology and evolution of these species.