There are several well-studied examples of protective symbiosis between insect-host and symbiotic actinobacteria, producing antimicrobial metabolites to inhibit host pathogens. These mutualistic relationships are best described for some wasps and leaf-cutting ants while a huge variety of insect species still remains poorly explored. For the first time we isolated actinobacteria from harvester ant Messor structor, and evaluated the isolates’ potential as antimicrobial producers. All isolates could be divided into two morphotypes of single and mycelial cells. We found that the highest frequency of occurrence of mycelial morphotype was observed among soldiers, and the lowest among larvae in the studied laboratory colony. The representative of this morphotype was identified as Streptomyces globisporus subsp. globisporus 4-3 by polyphasic approach. It was established using E. coli JW5503 pDualRep2 system, that crude broths of mycelial isolates inhibited a protein synthesis in reporter strains, but it did not disrupt the in vitro synthesis of proteins in cell-free extracts. Active compound was extracted, purified and identified as albomycin δ2. Pronounced ability of albomycin to inhibit the growth of entomopathogens suggests that Streptomyces globisporus subsp. globisporus may be involved in defensive symbiosis with the Messor structor ant against infections.