Unveiling the Hidden Complexity: Morphological Polymorphisms and Cryptic Diversity in a Zooxanthellate Massive Coral Species of the Genus <i>Favites</i> (Scleractinia, Merulinidae)

ABSTRACT The species‐level identification of zooxanthellate scleractinian corals based on morphology is extremely difficult. This difficulty can potentially lead to inaccurate conclusions due to species misidentification, posing a risk in applied research. In this study, we integrated detailed morphological and molecular phylogenetic analyses to investigate the hidden morphological polymorphisms of Favites valenciennesii , a species primarily characterised by the presence of groove‐and‐tube structures between corallites. Because F. valenciennesii shares morphological similarities with related taxa, its taxonomic status has remained unresolved for over 170 years. To address this, we combined Random Forest‐based feature selection with multivariate analysis to identify species‐specific morphological characteristics of F. valenciennesii . This approach classified F. valenciennesii into four morphologically distinct types (types A–D). Molecular phylogenetic analysis further revealed that two types (A and B) belong to the genus Favites , while the other two types (C and D) belong to Dipsastraea . Within Favites , two distinct clades corresponded to types A and B. Comparison with type specimens and taxonomic studies confirmed that type A represented true F. valenciennesii , while type B represented Favites irregularis comb. nov. Although types C and D were not formally described, the results suggested that they likely represent undescribed species of Dipsastraea . The integrated approach used in this study provides highly accurate species identification and offers significant potential for improving coral taxonomy.