Studies of antibacterial secondary metabolites of marine micromycete fungi as an element of a modern strategy for the search for new antibiotics are considered. More than half of the drugs currently used in practice have been isolated from bacteria (Bacteria) and actinomycetes (Actinomycetes); however, the first antimicrobial compounds were isolated from mycelial fungi (Ascomycetes), and it is obvious that their potential has not been exhausted. Marine fungi occupy a separate niche due to the peculiarities of their habitats, which also affect their production of low molecular weight compounds. This paper provides information on the secondary metabolites of marine fungi acting against those bacterial targets focused by the modern search for new antibiotics and discusses a strategy for investigating the antibacterial activity of marine fungal metabolites.