Stonefishes (Family: Synanceiidae) are venomous, benthic marine fishes with cryptic morphology and unresolved taxonomy. Despite their ecological and medical significance, they are poorly documented in Indian waters, particularly along the Kerala coast. This study employed an integrative approach, combining morphological and mitochondrial DNA analyses, to clarify species boundaries. Specimens were collected as bycatch from trawl landings at Munambam, Kalamukku, and Sakthikulangara (January–April 2025). Forty-seven morphometric measurements and five meristic counts were recorded per specimen. Mitochondrial DNA was extracted from muscle tissue, and the cytochrome c oxidase subunit I (COI) gene was amplified via PCR. Sequences were aligned, and phylogenetic relationships were inferred using the Maximum Likelihood method. Eight species were identified—Apistus carinatus, Inimicus didactylus, I. sinensis, Choridactylus multibarbus, Minous monodactylus, M. inermis, M. trachycephalus, and M. dempsterae. Morphological identifications were confirmed through DNA barcoding, with COI-based phylogeny revealing eight distinct clades and interspecific genetic divergence of 4.1–24.6% (mean: 19%). Distinct length–weight relationships were established for M. inermis and M. dempsterae. This first integrative taxonomic account of Synanceiidae from the Kerala coast demonstrates the value of combining classical and molecular tools for delineating cryptic marine species and provides a foundation for accurate biodiversity assessment, ecological monitoring, and conservation planning.