Abstract: Persistent taxonomic uncertainty has surrounded Engelhardia roxburghiana Lindley ex Wallich, E. fenzelii Merrill, and E. unijuga Chun ex P.Y. Chen, which have often been merged into a single species based on limited morphological interpretation. To resolve this controversy, an integrative reassessment of species boundaries was conducted using evidence from morphological traits, phylogenetic relationships, and ecological differentiation. Detailed morphological observations and statistical analyses demonstrated clear and stable differences among the three taxa: E. roxburghiana, branches fuscous, leaflets 3–5 pairs stably, rachis > 3.7 cm; E. fenzelii, branches white gray, leaflets two pairs stably and < three pairs, rachis 1.1–3.7 cm; E. unijuga, leaflets one pair, without rachis. Phylogenetic analysis suggested that the three species formed three independent branches, with E. fenzelii being more closely related to E. unijuga in terms of genetic relationships. Ecological niche analyses further indicated incomplete overlap in geographic distributions across China. Within a 60 hm² forest plot at Jianfengling, Hainan, distinct habitat differentiation was observed, with E. roxburghiana broadly distributed throughout the plot, E. unijuga largely confined to ridge habitats, and E. fenzelii absent from the sampled area. In summary, concordant morphological, phylogenetic, and ecological evidence supported recognition of E. roxburghiana, E. fenzelii, and E. unijuga as distinct species, thus restoring the species-level status of E. unijuga.