This study is aimed to isolate some novel probiotics from the soils of North East Himalayas. Eleven Gram positive isolates were obtained in MRS with Oxgall media from soil samples. Four of the isolates withstood the in vitro gastric juice pH 3.0 and 0.45% bile salt tolerance screening. Among these, PBT 3 showed high cell surface hydrophobicity and adhered to the Caco-2 cells. 16s rDNA gene sequences of this probiotic strains were identified as Bacillus amyloliquefaciens (accession no: JF836079). In in vivo bioefficacy evaluation by DSS-induced colitis animals, B. amyloliquefaciens significantly ameliorated the loss in body weight. Further, the treatment altered the levels of myeloperoxidase, lipoperoxides, and mucous content in the colon tissues compared with normal colon. It reduced the protein and mRNA levels of pro-inflammatory cytokines such as TNF-α and IL-1β. These biochemical findings were supported by histopathological evidences. Our study reports the use of B. amyloliquefaciens isolated from Himalayan soil as probiotic and its beneficial effect on IBD for the first time and suggests that this could be used as potential probiotics in functional foods or as a curative agent.