In the present study, hyper-xylanase producing novel bacterial strains were isolated from faeces of the Indian flying fox (Pteropus giganteus). Considering the qualitative assay, off 27 bacterial isolates, three strains were observed to be the hyper producers of xylanase. The potent isolates were identified using biochemical as well as molecular characterization tools, and were categorized under Bacillus spp. Further, the production of extracellular xylanase was quantified up to 72 h using standard methodology. The hyper production of xylanase was observed in the order of Bacillus amyloliquefaciens strain LAA64 (998.32 ± 17.6 U/mL) > B. methylotrophicus strain DLA64 (937.89 ± 16.1 U/mL) and > B. velezensis strain DLLA28 (910.46 ± 14.5 U/mL) at 48 h of incubation period. Evidently, these novel strains were identified as promising source for xylanase yield. Xylanase represents one of the most important groups of industrial enzymes and thus xylanases obtained from Bacillus spp. suggest their wide applications in diversified industries.