From 1988 to 1998, we collected flower heads of 39 thistle taxa (35 taxa of Cirsium, one species each of Breea, Synurus, Saussurea and Arctium; Cardueae; Astaraceae) in Japan, mainly from Hokuriku and other parts of central Honshu, and kept them in the laboratory to breed weevils and tephritid flies, the core fauna. We report the faunal make-up, host plants, geographic distribution and the attack levels of the insects. Results indicated that (i) three Larinus species (Curculionidae) and three species of tephritid flies (Tephritis, Urophora and Xyphosia) comprised the core fauna; (ii) two insect species belonging to the same taxonomic group (either Curculionidae (Larinus) or Tephritidae) tended to use different host plant species; (iii) two sympatric Larinus species (L. latissimus and L. meleagris) segregated the host plants seasonally in central Honshu (Cirsium blooming in spring and autumn, respectively); and (iv) two tephritid fly species, Xyphosia punctigera and Urophora sachalinensis, segregated geographically (the former on the Japan Sea side and the latter on the Pacific Ocean side). In comparison with their European counterparts, the weevils and tephritids of the Japanese Cirsium are characterized by a lower species richness and a lower degree of specialization in usage of the thistle flower heads, with gall-formers being distinctly under-represented, and callus tissue-feeders being absent. This reflects the fact that Japanese thistles are so closely related that hybridization frequently occurs, and also that the thistles have had a short history of interaction with the insects since the thistles’ arrival in Japan.