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<i>Fusarium graminearum</i> causing head scab (HS) or head blight (HB) disease in wheat is one of the nasty fungi reported to cause significant grain quality and yield loss. Biological control using endophytic bacteria has emerged as a prospective option for containing fungal diseases in an environmentally benevolent, durable, and sustainable manner. In this regard, 112 endophytic bacilli were isolated from the anthesis stage (Zadok’s growth stage 65) from five different wheat genotypes with an aim to identify prospective antagonistic strains against <i>F. graminearum</i>. The molecular identity of the strains was confirmed by matching 16S rRNA sequences of bacterial strains with the gene sequences of type strains available in the National Center for Biotechnology Information database and reported 38 different species of <i>Bacillus</i> in all the five wheat cultivars. Further, it has been observed that only fourteen strains (<i>B. clarus</i> NOK09, <i>B. mojavensis</i> NOK16, <i>B. subtilis</i> NOK33, <i>B. rugosus</i> NOK47, <i>B. mojavensis</i> NOK52, <i>B. clarus</i> NOK59, <i>B. coahuilensis</i> NOK72, <i>B. cabrialesii</i> NOK78, <i>B. cabrialesii</i> NOK82, <i>B. rugosus</i> NOK85, <i>B. amyloliquefaciens</i> NOK89, <i>B. australimaris</i> NOK95, <i>B. pumilus</i> NOK103, and <i>B. amyloliquefaciens</i> NOK109) displayed in-vitro antagonistic effect against <i>Fusarium graminearum</i> fungus. Furthermore, the three endophytic <i>Bacillus</i> strains showing the strongest antagonistic effect (>70% of growth inhibition of fungal mycelium) under in-vitro antagonistic assay were selected for field experiments. In a two-year consecutive field study, a combination of three strains (<i>B. clarus</i> NOK09 + <i>B. subtilis</i> NOK33 + <i>B. amyloliquefaciens</i> NOK109) displayed a remarkable reduction in HS disease index by 81.47% and 77.85%, respectively. Polymerase chain reaction assay detected three genes (<i>itu</i>D, <i>bmy</i>C, and <i>srf</i>A) involved in antibiotic biosynthesis pathways. Additional attributes such as potassium solubilization, siderophore release, and hydrolytic enzyme (protease, lipase, amylase, chitinase, and pectinase) synthesis have been observed in these strains. Overall, the present study was successful in profiling endophytic bacilli and selecting the combination of effective antagonistic endophytic <i>Bacillus</i> strains that could be the best alternative for the sustainable and ecological sound management of HS disease in wheat under field conditions.