Phomoxanthone A is a bioactive tetrahydroxanthone dimer found in many different fungal species. However, the complete biosynthetic pathway and the enzymatic 4,4′-linkage dimerization step remain mysterious. Here, we isolate a major secondary metabolite Phomoxanthone A, with 4,4′-linkage structure, from marine fungus Diaporthe sp. 4722. The biosynthetic gene cluster (BGC) for Phomoxanthone A, consisting of 20 genes, and among them 14 biosynthetic genes, was also identified by genome sequencing, qPCR analysis and gene-deletion experiments and the 14 biosynthetic genes were stepwise introduced into Aspergillus oryzae NSAR1, which enables us to isolate Phomoxanthone A and its 21 derivatives, and elucidate its complete biosynthetic pathway. Notably, an unusual dimerase, Cytochrome P450 PhoO, was uncovered, which exhibits high regioselectivity with 4,4′-linked dimerization under the condition of directing ortho-hydroxyl group free. PhoO reveals a novel enzymatic 4,4′-linkage dimerization method in tetrahydroxanthones, which should facilitate engineering the biosynthesis and structural diversity of novel 4,4′-linkage dimerization anthraquinones and structurally related analogues.