...little is known about the gut fungal dysbiosis caused by HIV-infection. ...we launched a case-control study aiming to explore the gut dysbiosis of bacteria and fungi in HIV infection, which may reveal a more comprehensive feature of HIV infection-related gut dysbiosis of bacteria and fungi that possibly play a role in the chronic systemic immune activation observed in HIV infection. According to the observed species (P < 0.0001), the alpha-diversity of fungi in HIV+ was marginally higher than that in HIV–. For bacteria in HIV+, 1) Dialister exhibited a positive correlation with two microbial translocation markers (sCD14 and MBP/MBL) and five inflammatory-related cytokines (IL-6, IL-17, IL-1β, IL-22, and IL-10), which may suggest Dialister play a dual role of pro-inflammation and anti-inflammation in HIV infection; 2) Fournierella, was positively associated with three microbial translocation markers (LPS, LBP and MBP/MBL) and four inflammatory-related cytokines (IL-17, TNF-α, IL-22, and IL-10); 3) negative correlation was found between Fusobacterium and LPS, sCD14, IL-6, IL-1β, and MBP/MBL. ...our findings contribute to a better understanding of the alterations in the gut bacterial and fungal microbiome and their associations with chronic systemic immune activation observed in HIV infection by providing a more comprehensive picture of HIV infection-related dysbiosis of the gut microbiome.