The highly dangerous trend of escalating bacterial resistance to modern antibiotics has evolved in recent decades, with increasingly more drug-resistant strains of pathogens emerging and spreading each year. This poses a threat to not only public health, but also to entire mankind. Marine bioresources, considered as a promising alternative to traditional antibiotics and a valuable source of biologically active compounds with high pharmacological potential, now attract increasing attention of researchers. Modern biotechnology combines the genetic engineering methods and the unusual biosynthetic pathways utilized by marine microorganisms to produce natural antibiotics. The goal of this review is to summarize the latest trends in searching for new natural antimicrobial agents based on secondary metabolites of marine bacteria. The targeted control of biosynthesis mechanisms using the metabolic engineering methods in order to create hybrid peptide synthetases or to obtain hybrid peptides by disrupting the target gene of nonribosomal synthesis becomes a noteworthy trend in modern biotechnology. This pathway is not only one of the most promising approaches to the development of new antibiotics, but also a potential target for controlling the exocrine activity of pathogenic bacteria and, consequently, their viability.