Polypeptide antibiotics are synthesized by Bacillus under control of nonribosomal polypeptide synthetases (NRPS). NRPS genes comprise the sequences of functional modules, each being responsible for incorporation of a certain amino acid to the synthesized oligopeptide. Dinucleotide frequency profiles calculated for DNA loci, covering the functional subunits of NRPS genes, were often observed to be significantly distant from those determined for the complete genome of the strain-producer, that suggests a possibility of horizontal transferring of the NRPS modules between microorganisms. A comparative analysis of the amino acid sequences of NRPS modules and statistical analysis of oligonucleotide usage frequencies allows following the pathway of evolution of genes controlling biosynthesis of antibiotics in Bacillus. A set of primers has been developed for genotyping of Bacillus strains with the purpose to identify producers of new polypeptide antibiotics among environmental isolates.