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To select isolates suitable for use in biological control of pathogenic fungi and as plant growth promoting (PGP) agents, Pseudomonas spp., indigenous to the rhizosphere of wild alfalfa and clover plants growing on the old magmatic hill Vagan (Serbia), were isolated. Isolates were selected on the basis of intrinsic antibiotic resistance (IAR) and PGP traits: phosphate solubilization, production of siderophores, hydrogen cyanide (HCN), acyl homoserine lactones (AHLs), indole acetic acid (IAA) and enzymatic activities. The results of the genotyping by repetitive sequence-based polymerase chain reaction, using ERIC and (GTG)(5) primers, and phenotyping by IAR clustered the isolates in five groups, represented by two isolates from alfalfa (Q1 and Q16) and three from white clover (B25, B28 and B29). Isolates Q16 and B25 showed production of HCN, IAA and AHLs. Good phosphate solubilization and production of siderophores were observed on Q1 and Q16. The Q16 isolate exhibited high enzymatic activity. The most promising PGP isolates, Q16 and B25, showed the best antifungal activity against Trichoderma viride, and good antifungal effect against Aspergillus fumigatus and Aspergillus niger, while Penicillium verrucosum was the most resistant fungus. Pseudomonas sp. B25 exhibited higher antifungal potential than Q16. The selected isolates could be further investigated as biological control agents and tested in field conditions to confirm their PGP efficacy.