The hepato-intestinal schistosomosis, a chronic debilitating infection caused by Schistosoma indicum is one of the major helminthic problems which cause considerable reduction in production and productivity, and economic losses in Assam, India. Hence their accurate diagnosis by traditional and molecular methods is the key to its management. A total of 420 faecal samples and liver and intestinal mesenteries from different slaughter houses of Assam were collected and examined during March 2015 to February 2016 to record the prevalence of visceral schistosomosis. It was observed that prevalence rate of schistosomosis was found to be more in mesenteric and hepatic portal vein examination (12.38%) than the faecal examination (4.52%). The 28S RNA gene (28S) and mitochondrial cytochrome c oxidase subunit 1 (COI) gene of morphologically identified adult S. indicum was amplified with amplicon sizes 590 bp and 372 bp, respectively which could be used as molecular marker for diagnosis S. indicum infection. However, based on worm pair detection, the study showed an increasing incidence of schistosomosis from the month of May onward reached highest peak in July and gradually decline to lowest point in April, while coprological examination showed the highest peak in August and the lowest in March. The risk factors include age, breed and management systems of the cattle. Therefore, this study emphasizes on employing both conventional and molecular techniques to detect the various risk factors of S. indicum infection in cattle for successful control measures.