Abstract: The mushroom corals (Fungiidae) are not only key components of biodiversity in coral reef ecosystems, but their unique life-history strategies and morphological characteristics also provide important models for studying coral evolution and environmental adaptation. However, systematic investigations of Fungiidae in the northern and central South China Sea (including the Xisha Islands, Zhongsha Atoll, and waters surrounding Hainan Island) have long been lacking. From 2020 to 2025, our research team conducted continuous field surveys and specimen collections in the Xisha Islands, Zhongsha Atoll, and around Hainan Island. Notably, the 2023, 2024, and 2025 expeditions represented the first systematic sampling and investigation of mesophotic Fungiidae in the Xisha Islands. Based on accumulated specimens from multiple years, and integrating morphological characteristics with molecular phylogenetic evidence, a total of 12 genera and 20 species were identified from the Xisha Islands, 12 genera and 13 species from Zhongsha Atoll, and 3 genera and 3 species from Hainan Island. Six genera and nine species are newly recorded in the Xisha Islands, among which three species are mesophotic specialists. This highlights the previous insufficiency of surveys on Fungiidae in this depth zone. Additionally, two genera and six species are newly recorded in Zhongsha Atoll, and two genera and two species are newly recorded around Hainan Island. During species identification, we found that Danafungia danai, which had long been synonymized with Danafungia horrida, formed two distinct clades in phylogenetic trees constructed using COI, ITS, and 13 mitochondrial protein-coding genes, with significant morphological differences. It should therefore be resurrected as a valid independent species. Bayesian phylogenetic analysis based on 13 mitochondrial protein-coding genes further revealed that the family Fungiidae can be divided into four major phylogenetic clades (Clade I-IV). Interestingly, except for Clade IV, the mitochondrial genomes of the other clades all contain minisatellite repeat sequences. These repeat sequences may serve as high-resolution molecular markers for population genetics and phylogenetic studies.

Key words: Fungiidae, Species diversity, Phylogeny, Mitochondrial genome, Minisatellite repeats