Parasitic infections of small ruminants are one of the major concerns and cause significant losses to the livestock industry in India. Accurate diagnosis of the parasitic diseases are essential to study the epidemiology, parasite control strategies, which assists in the improving the productivity of sheep in world wide. However, current routine diagnostic techniques have limitations, in sensitivity and/or specificity, which hamper efforts to investigate the epidemiology of key species. Development of the drug resistance in parasites of sheep, is a major need for advanced methods of diagnosis. Diagnosis of parasitic diseases is regularly done by conventional methods, but DNA based approaches of diagnosis can overcome the disadvantages of previous methods. To assess the molecular and genetic host parasitic interaction different advanced molecular tools are required and it is useful in the diagnosis of parasitic diseases. Various molecular diagnostic techniques that have been developed for diagnosis of parasites include conventional PCR, RAPD-PCR, RFLP-PCR, multiplex-PCR, real-time PCR, reverse transcriptase PCR, Nested PCR, In Situ PCR, SSCP-PCR PCR-ELISA, RLB, micro-arrays, LAMP and microsatellite etc.