Gastrointestinal(GI)parasitism is the most serious constraint throughout the world in small ruminants which causes significant production loss in animals.GI parasites are major contributor to reduce productivity in terms of meat, milk and wool in animals. Control ofGI parasite is done primarily by anthelmintic treatment where choice and schedule of treatment is done after identification and quantitation of individual parasite. Identification ofGI parasites is done through microscopic method by identifying specific morphological characteristics of egg and larva (L3). Since most of parasite eggs are having similar morphological characteristics, identification up to species level through microscopy is not possible in most of cases. To address this issue, molecular techniques are the viable altative for identification of species as well as molecular level differences within a species (isolates) of parasites. DifferentDNA based molecular techniquesviz.PCR, AFLP, RAPD, RFLP, PCR-SSCP, real timePCR, DNAmicroarrayetc. have been used for identification and to assess the genetic diversity among parasite population. For identification of species, the characteristic sequence of genomicDNAof different species should differ to allow the delineation of species, but at the same time, no/minor variation within the species should exist. In contrast, for purpose of identifying population variants (strains/isolates), a considerable degree of variation in the sequence should exist within a species. Various target regions, including nuclear ribosomal DNA (rDNA), mitochondrial DNA(mtDNA) or repetitiveDNA elements (microsatellite loci), which show considerable variation in the number of repeats within individuals have been employed to achieve the identification of parasites species or strain.