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Biofilm-associated <i>Candida albicans</i> infections, the leading cause of invasive candidiasis, can cause high mortality rates in immunocompromised patients. Photodynamic antimicrobial chemotherapy (PACT) is a promising approach for controlling infections caused by biofilm-associated <i>C. albicans</i>. This study shows the effect of Elsinochrome A (EA) against different stages of <i>C. albicans</i> biofilms in vitro by XTT reduction assay and crystal violet staining. The mechanism of action of EA on <i>C. albicans</i> biofilm was analyzed with flow cytometry, confocal laser microscopy, and the Real-Time Quantitative Reverse Transcription PCR (qRT-PCR). EA-mediated PACT significantly reduced the viability of <i>C. albicans</i>, with an inhibition rate on biofilm of 89.38% under a concentration of 32 μg/mL EA. We found that EA could not only inhibit the adhesion of <i>C. albicans</i> in the early stage of biofilm formation, but that it also had good effects on pre-formed mature biofilms with a clearance rate of 35.16%. It was observed that EA-mediated PACT promotes the production of a large amount of reactive oxygen species (ROS) in <i>C. albicans</i> and down-regulates the intracellular expression of oxidative-stress-related genes, which further disrupted the permeability of cell membranes, leading to mitochondrial and nuclear damage. These results indicate that EA has good photodynamic antagonizing activity against the <i>C. albicans</i> biofilm, and potential clinical value.