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In this study, a strain of siderophore-producing endophytic bacterial strain, HS-4, was isolated using improved sugar-aspartic acid (MSA) as a selective medium. The antifungal effect of this bacteria was then assessed against cotton wilt pathogen (Fusarium oxysporum) at varying concentrations of FeCl3. This strain was identified using morphological, biochemical and physiological characteristics, 16S rDNA sequence homology and phylogenetic analysis. Strain HS-4 produced fluorescent siderophores in MSA medium, the relative content of which amounted to 80%. The siderophore produced by strain HS-4 exhibited significant inhibitory activity against F. oxysporum growth under low iron conditions. Strain HS-4 was identified as Bacillus atrophaeus.