Larvae of Bradysia agrestis, a phytopathogen-transmitting insect vector in East Asia, were sampled from geographically (ecologically) segregated regions to identify their intestinal fungal flora. A total of 24 fungal strains were isolated from the insect vectors and selected based on morphological differences. In addition, 38 fungal strains were isolated from the ulcerated parts of invaded host plants by the same method, revealing the impact of vector fungal flora on their host plants. For molecular identification of the fungi, internal transcribed spacer (ITS) regions were amplified and sequenced. Their sequences were compared with sequences of other fungal strains obtained from NCBI GenBank, and their phylogeny was determined. The dominant fungal genera in the insect vector were Penicillium (25%), Aspergillus (21%), and Cladosporium (13%). In plant scar lesions, most fungal isolates belonged to the genera Fusarium (31.6%), Phoma (7.8%), Didymella (7.8%), and Epicoccum (7.8%). Fungal genera in vectors or host plant lesions differed by study site. Furthermore, diversity indices by study site showed clear differences based on Margalef’s richness (2.06, 2.40, 3.04), and Menhinick’s (1.89, 2.12, 2.53), and Simpson’s indices (0.14, 0.07, 0.07). In addition, common fungal strains in insect vectors were found to be closely related to members of the genera Cladosporium, Penicillium, or Aspergillus. Among these strains, those showing the highest homology with Aspergillus terreus, which regarded as beneficial fungal genera could be considered ideal paratransgenesis candidates. Some other fungal strains from vectors or ulcerated plant parts from each study site after B. agrestis invasion may be harmful in terms of plant disease or agrifood safety. This study provides information on the fungal microbiota of B. agrestis, an emerging problem in East Asia, and proposes paratransgenesis candidates to control this insect vector. Furthermore, potential transferable pathogens or commensal fungi were revealed by comparing the fungal biota between the insect gut and the ulcerated parts of the invaded host plants.