Mesopelagic fishes experience an extreme body transformation from larvae to adults. The identification of the larval stages of fishes from the two orders Myctophiformes and Stomiiformes is currently based on the comparison of morphological, pigmentary and meristic characteristics of different developmental stages. However, no molecular evidence to confirm the identity of the larvae of these mesopelagic species is available so far. Since DNA barcoding emerged as an accurate procedure for species discrimination and larval identification, we have used the cytochrome c oxidase 1 or the mitochondrial 12S ribosomal DNA regions to identify larvae and adults of the most frequent and abundant species of myctophiforms (family Myctophidae) and stomiiforms (families Gonostomatidae, Sternoptychidae and Phosichthyidae) from the Mediterranean Sea. The comparisons of sequences from larval and adult stages corroborated the value of the morphological characters that were used for taxonomic classification. The combination of the sequences obtained in this study and those of related species from GenBank was used to discuss the consistency of monophyletic clades for different genera. Pairwise nucleotide distances were notably higher inter- than intraspecifically, and were useful to discern between congeners such as Cyclothone braueri and C. pygmaea, Hygophum benoiti and H. hygomii, Lampanyctus crocodilus and L. pusillus, and Notoscopelus bolini and N. elongatus.