Directional asymmetry indicates a unidirectional deviation from perfect bilateral symmetry, which was rarely examined in the inner organs of the teleost (Teleostei) compared to external traits. This study examines the directional asymmetry in the gonad length of 20 species of moray eels (Muraenidae) and two outgroup species with 2959 individuals. We tested three hypotheses: (1) moray eel species did not exhibit directional asymmetry in the gonad length; (2) the directional asymmetry pattern was the same for all selected species; (3) the directional asymmetry was not related to the major habitat types, depth and size classes, and taxonomic closeness of the species. Moray eels were generally “right-gonadal”, the right gonad length being constantly and significantly longer than the left one in all studied Muraenidae species. The degree of asymmetry varied among species and was not significantly related to taxonomic closeness. The habitat types, depth, and size classes had intermingled effects on observed asymmetry without a clear correspondence. The directional asymmetry in the gonad length is a unique and widely occurring phenomenon in the Family Muraenidae, which was likely a by-product in the evolutionary history without significant disadvantage in survival.