Achieving metabolomic data with satisfactory coverage is a formidable challenge in metabolomics because metabolites are a chemically highly diverse group of compounds. The knowledge concerning the behavior of these Bacilli as antagonists and metabolite analysis is essential for their effective use and the commercialization. The present study was focused on selection of best biocontrol antifungal Bacillus strain against aflatoxin producing Aspergillus by antagonism on PDA medium. About 16 different strains of bacteria were isolated from healthy and infested rhizosphere of groundnut using N-agar medium. The isolates were identified based on morphological and microscopic characters. Bacterial isolate JND-KHGn- 29-A and JND-KSGn-30-L were recorded to be a best antagonist as of its ability to inhibit most toxic fungus A. flavus JAM-JKB-BHA-GG20 (58.20%) after screening with 16 Bacillus isolates. GCMS analysis of best and least bacterial antagonist Bacillus subtilis (JND-KHGn-29-A, Accession KU984480) inoculated onto N-agar medium identified total 55 and 42 compounds respectively. Whereas GCMS analysis from best bacterial antagonist Pseudomonas isolate no. 14 (JNDKSGn- 30-L) inoculated onto N-agar identified total 60 compounds.