This paper describes the species composition and the relative dominance of the associated fungi in the gallery system and in the mycangium of three ambrosia beetles (Scolytophathpus mikado Blandford, Xylosandrus crassiusculus (Motschulsky), and X. brevis (Eichhoff)) by analyzing the changes with the developmental stages of the beetle. Both isolation experiments and scanning electron microscopy were employed. The isolated fungi were classified into three groups: Ambrosiella spp., yeast-like fungi, and other fungi (mainly Paecilomyces sp.). Ambrosiella spp. were highly species-specific among scolytid species; Ambrosiella sp. 1, sp. 2, and sp. 3 were isolated from Scolytoplatypus mikado, Xylosandrus crassiusculus, and X. brevis, respectively. Ambrosiella spp. were generally predominant among the fungal groups in the egg/larval periods in the galleries and mycangia of each beetle species. Yeast-like fungi were constantly isolated from the galleries. These results suggested that the symbiotic fungi associated with the three ambrosia beetles were species-specific Ambrosiella spp., and associated yeast-like fungi were likely to be auxiliary ambrosia fungi.