The stomatopod family Gonodactylidae Giesbrecht, 1910 comprises ecologically important predators in coral reef ecosystems, yet its phylogenetic relationships remain poorly resolved, particularly within the genus Gonodactylellus Manning, 1995. Despite the growing number of known species in this genus, research in the South China Sea (SCS)—a widely recognized marine biodiversity hotspot—remains limited. To address these gaps, we performed an integrative taxonomic analysis of 53 gonodactylid specimens collected from the SCS, combining detailed morphological examinations with molecular species delimitation based on the COI barcode gene. Our results revealed substantially underestimated diversity within Gonodactylellus in the SCS, including a new record of Gonodactylellus caldwelli Erdmann & Manning, 1998 in the region, and two phylogenetically distinct lineages representing new species: Gonodactylellus xishaensis sp. nov. and Gonodactylellus sp. We further reconstructed the phylogeny of Gonodactylidae by incorporating mitochondrial genomes (mitogenome) and nuclear genes (18S rRNA, 28S rRNA and H3), including nine newly generated and four previously published gonodactylid mitogenomes. All phylogenetic reconstructions, including those based on an extensive COI dataset with wide taxon coverage and those using a reduced taxon set with multi-gene dataset, consistently rejected the monophyly of Gonodactylellus, with Gonodactylus Berthold, 1827 nested within it, indicating a close affinity between these two genera. These findings highlight the SCS as a reservoir of previously underestimated gonodactylid diversity and underscore the persistent phylogenetic complexity of Gonodactylellus.