Fish is an important part of the human diet. The people of Manipur extensively consume fish as a staple food. Parasites in fish are a common natural occurrence. Among the parasites, helminths are known to harm the hosts and some of them are also well known for their zoonotic potential. However, reports on the study of helminths in fishes from this region are limited. The present work was undertaken to study the species composition, identification of the helminths and to evaluate the seasonal variation in prevalence, abundance and mean intensity of helminths occurring in the common edible fishes of Manipur. For identification and characterization, light microscopic and scanning electron microscopic study of helminth parasites were undertaken. Gene sequencing for three commonly used molecular markers, i.e., nuclear ribosomal internal transcribed spacer 2 (rDNA-ITS2), 18S (or small subunit- SSU) and mitochondrial cytochrome c oxidase subunit 1 (mtCO1) was also carried out for identification and characterization. The quantitative descriptors like prevalence, abundance and mean intensity were estimated using the methods formulated by the American Society of Parasitologists. From the present study, it is revealed that among the fish-borne helminth parasites, Clinostomum metacercariae and Anisakis sp. emerged as the potential zoonotic trematode prevailing in Manipur, North East India. A temperature range of 24-27 degree Celcius revealed to be favourable for infection of helminth parasites. Therefore, we suggest that treatments should be provided during the monsoon and pre-monsoon seasons, which might prove to be effective in controlling the helminth infections.