Fishes of the Mugilidae family are poorly known from a taxonomic perspective, largely because of their conservative morphology. In this paper, we aim to fill the knowledge gap and data deficiency regarding the genetic diversity of mullets occurring in southern peninsular India. A comprehensive mitochondrial phylogeny based on 238 COI sequences (78 newly generated) and three species delimitation methods (ASAP, RESL, and ABGD) confirmed the presence of 21 species of mullets within eight genera in southern peninsular India. These include one species each under the genera Rhinomugil Gill 1863, Minimugil Durand, Chen, Shen, Fu, and Borsa, 2012, Plicomugil Schultz 1953, and Ellochelon Whitley 1930; seven species of Planiliza Whitley 1945; four species of Crenimugil Schultz 1946; four species of Osteomugil Luther 1982; and two species of the “Mugil cephalus Linnaeus 1758” complex—though with uncertainty regarding the exact geographic origin of one of the two species of the “Mugil cephalus” complex and one species phylogenetically close to Planiliza subviridis (Valenciennes 1836). We provide an overview of the specific geographical regions in southern peninsular India, and “species groups”, which require future research using an integrative approach, so as to unravel the true extent of mullet diversity and their distribution in the region.