Paragonimiasis, a crustacean borne trematodiasis caused by lung flukes of the genus Paragonimus. Among the species, Paragonimus westermani are an important parasite causing clinical manifestation similar to that of pulmonary tuberculosis. So, the knowledge on their phylogenetic analysis, genetic variation, conserved regions within the isolates can bring out information regarding distribution and specific genes responsible for pathogenecity, which can be utilized in control programmes. In Manipur, North East India, freshwater crab (Barythelphusa lugubris) has been consumed as a local delicacy by endemic people of the region. They are found harbouring with P. westermani metacercaria. The freshwater crab host from the susceptible loci were collected and their genomic DNA was extracted followed with amplification of genetic marker ribosomal DNA ITS2 region. The desired genetic marker were sequenced and analysed for genetic variation, conserved regions and phylogenetic tree construction using various bioinformatics tools of BLAST, ClustalW embedded in Bioedit and MEGA11. The genetic variation analysis revealed the Paragonimus metacercaria under studies show 100% sequence identity with the isolates from the India states of Arunachal Pradesh and Assam, with only one conserved region of 338 base lengths. The phylogenetic tree constructed reveals the sequence cladding with the isolates of P. westermani from different geographical regions. Among the P. westermani isolates, eight conserved regions were depicted, and can be used as a target for drugs in control programme.