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Two actinomycetes isolates RK-302 and RK-320 obtained from limestone rock of Dehradun, Uttarakhand were characterized morphologically, biochemically and by using 16S rDNA sequencing at Jaypee Institute of Information Technology, Noida during 2017-18. Differences in morphological/biochemical features showed that the isolates differed from each other as well as from the nearest matching strains in the GenBank database. Variation in dimension for spore size of both isolates was observed through transmission electron microscopy. Both isolates, RK-302 and RK-320 showed activity against phytopathogenic fungi, Fusarium graminearum and Bipolaris maydis using agar plugs in vitro. Metabolite fingerprinting with GC-MS revealed the presence of 37 and 31 compounds, respectively from RK-302 and RK-320. Combined analysis of phenotypic, biochemical and molecular studies showed that the isolates differed at strain level. From the metabolite fingerprint and antimicrobial activity data, it was concluded that the antimicrobial compounds identified in present study may be useful in developing novel bio control agents for plant pathogens.