It is believed that wood-rot fungi change their wood decay activities due to influences from co-existing bacterial communities; however, it is difficult to elucidate experimentally the interaction mechanisms in fungal-bacterial consortia because the bacterial community structure is quite unstable and readily changes. Indeed, the wood decay properties of fungal-bacterial consortia consisting of a white-rot fungusPhanerochaete sordidaYK-624 and a natural bacterial community changed dramatically during several sub-cultivations on wood. Therefore, development of a sub-cultivation method that imparts stability to the bacterial community structure and fungal phenotype was attempted. The adopted method using agar medium enabled maintenance of fungal phenotypes relating to wood decay and the bacterial community even through dozens of repetitive sub-cultures. Some bacterial metabolic pathways identified based on gene predictions were screened as candidates involved inP. sordida–bacterial interactions. In particular, pathways related to prenyl naphthoquinone biosynthesis appeared to be involved in an interaction that promotes higher lignin degradation selectivity by the consortia, as naphthoquinone derivatives induced phenol-oxidizing activity. Based on these results, it is expected that detailed analyses of the relationship between the wood-degrading properties of white-rot fungal-bacterial consortia and bacterial community structures will be feasible using the sub-cultivation method developed in this study.