Abstract Antimicrobial photodynamic therapy (APDT) is a promising alternative to traditional antibiotics for bacterial infections, which inactivates a broad spectrum of bacteria. However, it has some disadvantages including poor water solubility and easy aggregation of hydrophobic photosensitizers (PS), and poor tissue penetration and cytotoxicity when using UV as the light source, leading to undesired photodynamic therapy efficacy. Herein, we develop a novel water-soluble natural PS (sorbicillinoids) obtained by microbial fermentation using recombinant filamentous fungus Trichoderma reesei ( T . reesei ). Sorbicillinoids could effectively generate singlet oxygen ( 1 O 2 ) under ultraviolet (UV) light irradiation, and ultimately display photoinactivation activity on Gram-positive bacteria, but not Gram-negative ones. Staphylococcus aureus ( S . aureus ) treated with sorbicillinoids and UV light displayed high levels of intracellular reactive oxygen species (ROS), notable DNA photocleavage, and compromised cell semi-permeability without overt cell membrane disruption. Moreover, the dark toxicity, phototoxicity or hemolysis activity of sorbicillinoids is negligible, showing its excellent biocompatibility. Therefore, sorbicillinoids, a type of secondary metabolite from fungus, has a promising future as a new PS for APDT using nontoxic dose of UV light irradiation. Importance It is of great value to develop novel PSs for APDT to enhance its efficacy for the reason that many traditional PSs have disadvantages like low water solubility and poor biocompatibility. In this study, we develop a novel water-soluble natural PS - sorbicillinoids obtained by microbial fermentation using T. reesei. Sorbicillinoids could effectively generate singlet oxygen under UV light irradiation, and ultimately display photoinactivation activity on Gram-positive bacteria, but not Gram-negative ones. More importantly, UV light can generally only be used to inactivate bacteria on the surface due to its weak penetration. However, it can penetrate deep into the solution and inactivate bacteria in the presence of sorbicillinoids. Therefore, sorbicillinoids, a type of secondary metabolite from fungus, has a promising future as a new PS for APDT using nontoxic dose of UV light irradiation.