Anthracnose is one of the most severe post-harvest diseases in mango fruits. Species of the Colletotrichum fungus cause it, affecting the quality of the fruit and, consequently, its commercialization. The current disease handling is based on frequent spraying of synthetic fungicides. However, their extensive and intensive use has disturbed the ecological balance of microorganisms present in the habitat, thus resulting in the development of resistant pathogenic strains, pollution of the environment, and risks to human health. As a handling alternative, extracts from six marine bacteria were evaluated against four Colletotrichum strains. The bacteria Bacillus velezensis INV FIR31, Bacillus subtilis INV FIR48, and Bacillus safensis INV FIR26 inhibited the mycelial growth of the strains by 40, 34, and 21%, respectively. Then, the antifungal activity of the extracellular extract BS57 obtained from B. velezensis INV FIR31 was evaluated in mango fruits of the Hilaza variety inoculated with Colletotrichum strains, obtaining disease percentages control of 42, 89, 91, and 92%. Finally, the lipopeptide Bacillomycin D in the BS57 extract was identified, indicating it was possibly responsible for the antifungal activity. Additionally, the toxicity tests of the extract show low toxicity. The results suggest that the extract obtained from the marine bacterium Bacillus velezensis INV FIR31 is a good resource for developing effective biopesticides that are environmentally friendly and safe for the consumer.