Abstract The Mariana Trench is the deepest of the world's deep‐sea trenches. To date, our knowledge of the fungal metabolism and biogeochemical cycles in the Mariana Trench biosphere is very limited compared with the Mariana Trench prokaryotes. Here, we collected the sediment cores from three layers (surficial 0–6 cm, intermediate 6–12 cm, and deep 12–18 cm) at eight stations in the abyssal–hadal transition zone of the Mariana Trench to investigate the sediment fungal community and biogeochemical potentials using metagenomics. Eight fungal phyla were detected, with Ascomycota being the most abundant, followed by Mucoromycota and Basidiomycota, along with the unique representatives Microsporidia and Rozellomycota (Cryptomycota). Distinct fungal community and biogeochemical potentials of carbon, sulfur, and nitrogen in the fine scale of the different sediment layers were revealed, while no obvious difference was detected between the southern and northern slopes of the abyssal–hadal transition zone of the Mariana Trench. In particular, the assimilatory sulfate reduction (ASR) pathway, including sat and cysI , cysC/PAPSS catalytic processes, as well as the dissimilatory nitrite reduction to ammonia by NIT‐6 , were highlighted based on the fungal metagenome. These results suggest sediment depth–dependent fungal community and biogeochemical potentials, providing novel insights into the less well‐known fungal microbiome in the Mariana Trench, particularly fungal different pathways from prokaryotes.