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Background: Heteraxinoides atlanticus Gayevskaya et Kovaleva (1979) is described from the locality of Arabian Sea, India. This monogenean species is first time reported from India, infesting the gills of Nemipterus japonicus (Bloch). The present study redescribes H. atlanticus and its phylogenetic status using morphometric and molecular tools. Methods: A total of 35 parasites were collected from the 234 specimens of Nemipterus japonicus at Mumbai, India. The temporary and permanent mounts were prepared for the morphometric analyses of H. atlanticus. For PCR, the genomic DNA was isolated from the parasites using primers for 18S rDNA, 28S rDNA and mtCOI gene. The obtained DNA sequences were subjected to different bioinformatics softwares (BLASTn, Clustal Omega and MEGA) for phlyogenetic analyses. Result: Phylogenetic analyses with the help of partial 18S and 28S rDNA sequences of H. atlanticus and other available sequences of heteraxinids provided the better understanding of relationship in the family Heteraxinidae. Another species, H. karachiensis Hadi and Bilqees (2014) showed similar morphological features such as number of clamps and structure of genital atrium to H. atlanticus except few minor differences, so it must be considered as synonym of H. atlanticus and placed into Heteraxinidae instead of Axinidae. [ABSTRACT FROM AUTHOR]