Pathogens isolated from fish appear to possess considerable antimicrobial resistance and represent a problem for the economy and public health. Natural antimicrobial substitutes to traditional antibiotics represent an essential tool in the fight against antibiotic resistance. Nanotechnology has shown considerable potential in different research fields, and the antimicrobial properties of silver nanoparticles are known. Silver has been used for medical purposes since ancient times because of its bactericidal properties, and the highly reactive surfaces of silver nanoparticles (AgNPs) indicate that they might have a function in antimicrobial applications. This work aimed to study the antimicrobial properties of biologically produced AgNPs from Origanum vulgare leaves compared to chemically produced AgNPs. Both types were characterized by UV–vis spectrophotometry, TEM, and dynamic light scattering and tested against three bacterial strains (Streptococcus agalactiae, and Aeromonas hydrophila, both isolated from Nile tilapia and Vibrio alginolyticus, isolated from sea bass) and three fungal strains (Aspergillus flavus, Fusarium moniliforme, and Candida albicans, all isolated from Nile tilapia). Disk diffusion test and evaluation of ultrastructure changes of tested microorganisms treated with AgNPs by transmission electron microscopy were performed. Moreover, the hemolytic properties of AgNPs were studied on chicken and goat red blood cells. The results obtained declare that the green biological production of silver nanoparticles is safer and more effective than the chemical one; moreover, AgNPs have interesting dose-dependent antimicrobial properties, with better results for biologically produced ones; their effectiveness against tested bacterial and fungal strains opens the way to their use to limit fish diseases, increase economy and improve human health.