We describe the results of three different approaches to the search for novel antimicrobial compounds in halophilic and halotolerant microorganisms inhabiting three different types of extreme ecosystems. By analyzing the metagenomes of microbial communities of underground thermal mineral waters, we identified clusters of biosynthesis of potential antimicrobial compounds belonging to archaea and actinobacteria of new uncultured groups. Enrichment cultures with antimicrobial activity were obtained from cold deep ocean sediments, and analysis of their phylogenetic diversity allowed us to identify potential producers of antimicrobial compounds as representatives of the Desulfuromonadia class. Finally, we characterized the antimicrobial activity of a new species of soil natronophilic Streptomyces sp. ACA25, which appears only against Gram-positive bacteria.