Despite the ecological and commercial importance of grey mullets (fish family Mugilidae), their taxonomy and systematics are still much debated. Reasons for this are the low level of morphometric variability and the relatively poor phylogenetic information borne by the morpho-anatomical characters used thus far in diagnosing species. Here, we evaluate the potential of DNA barcoding to accurately delineate species and assign unknown specimens to taxa in the family Mugilidae. Our reference sample consists of 257 individuals from 91 lineages characterized by their nucleotide sequences at the COI, cytochrome b, and 16S rRNA loci. These lineages correspond to 55 species according to the current taxonomy, and 36 presumed cryptic species. All known and presumed cryptic species within the ‘Mugil cephalus’ (n = 15) and ‘M. curema’ (n = 6) species complexes, as well as within genera Chelon (n = 10), Crenimugil (n = 6), Osteomugil (n = 6), and Planiliza (n = 18) were successfully recovered as distinct lineages by COI gene sequences (598 bp), demonstrating the utility of this marker to delineate species in the family Mugilidae. Inconsistencies in the labeling of sequences deposited in GenBank were ascribed to species misidentification. A proportion of these misidentifications occurred in the course of dedicated barcoding surveys, further emphasizing the need for an accurate and exhaustive reference barcoding database for Mugilidae.