New data about ecology, systematics and synthesis of biologically active substances of the type strain Pseudomonas batumici UCM-321 producing the antibiotic batumin, highly effective against staphylococci, and of Alteromonas macleodii strains, as representatives of marine species widely inhabiting the world ocean, was obtained based on a complex analysis of their biological properties and genomic structure. Analysis of taxonomic data indicated that P. batumici is a novel species. Illumina HiSeq sequencing of the chromosomal DNA enabled to obtain the complete genome sequence of P. batumici UCM B-321. Its DNA contained 127 contigs of the total length of 6608172 bp. Batumin biosynthesis operon was identified as 77 kbp operon containing in total 28 protein coding genes. This operon sequence was significantly less GC-rich and the program SeqWord Genomic Island Sniffer predicted a horizontal acquisition of this region. The closes relatives of UCM-321 were P. gingeri and P. protegens; both have no batumin operon in their genomes. HLPC-analysis of the culture broth has shown the presence of batumin in P. batumici broth and no any similar substances in P. gingeri culture medium. The phenotypic, chemotaxonomic and genetic peculiarities of 5 deep-water strains of A. macleodii (isolated from a depth of 1000–3500 m) and 5 strains of the same species isolated from the surface layer have been studied. Electron microscopy has shown that the deep strains’ cells were, on average, two times longer (2.1±0.2×0.7±0.1 μm) than the surface strains (1.1±0.1×0.6±0.1 μm). Using fatty acid analysis the deep and surface isolates were clearly separated into two clusters. The distinctions between them were also found in different lectin binding capacity, which was probably determined by the structure of their extracellular polysaccharide matrix. Analysis of the PCR results with the primers to repeated nucleotide sequences revealed a higher level of genetic polymorphism in surface strains in comparison to the deep-water isolates. The described peculiarities probably reflect the specific conditions in which A. macleodii strains live on the surface or in the depth of the World Ocean.