Anguillid leptocephali of three Congridae species (Conger conger, Ariosoma balearicum and Gnathophis mistax) were caught as bycatch of pelagic trawls during acoustic surveys targeting small pelagic fish species in the southern Adriatic Sea, carried out under the framework of the Italian MEDIAS project (western side) and its extension in the ambit of the FAO AdriaMed project (eastern side). Results refer to the findings of Congridae leptocephali during surveys conducted in 2011, 2014, 2015 and 2016. A total of 25 specimens were caught and analysed (morphological features and pigmentation patterns). Leptocephali of Conger conger were found in the range of 8.4–13.1 cm total length (TL) (between 50 and 132 m depth), Ariosoma balearicum from 9.7–12.2 cm TL (between 50 and 128 m depth) and for Gnathophis mystax in the range from 6.4–11.7 cm TL (between 40 and 79 m depth). The results indicate that the southern Adriatic Pit could be the spawning area of these species in the Adriatic Sea. Present data represent a contribution to existing knowledge about the ecology of leptocephali from the Congridae family in the southern Adriatic Sea, and also indicate the existence of differences in morphometric parameters between different areas, that is, the possibility of the existence of new geographic lines within the genus Ariosoma in the Adriatic Sea.