Phenovariant is a pair of populations or species with distinct phenotypes but little to no genetic divergence, which may have resulted from strong assortative mating, hybridization, or incomplete lineage sorting that changes in the phenotype have exceeded the genotype. Previous studies had mainly tackled this issue on small, colourful reef fishes, but little effort has been made to the barely seen and solitary taxa like the morays (family Muraenidae). In the present study, three species pairs of sympatric morays from Taiwanese waters revealed as phenovariant in the mitochondrial cytochrome oxidase I (COI) were examined from the molecular and morphological perspectives, with three dissimilar scenarios discovered: (1) no hybridization was found between the morphologically most distinct
Gymnothorax intesi and Gymnothorax neglectus;(2) Gymnothorax kidako bidirectionally hybridized with Gymnothorax prionodon instead of its closely related species Gymnothorax pseudokidako; and (3) frequently bidirectional hybridization and introgression were detected between Gymnothorax pseudothyrsoideus and Gymnothorax reevesii, a species pair that overlapped in all the morphometric and meristic characters. Nevertheless, the principal component analysis indicated that each species pair has evolved significant morphological divergence, further supporting their taxonomic validities. Our results document the natural hybridization of marine eel taxa for the first time and reveal a diverse evolutionary process among the morays.