Hindeodus parvus and Hindeodus typicalis occur in a deep-water chert and claystone section in the Mino Terrane, Japan, which has been identified as a Jurassic accretionary complex. Conodont fossils are preserved as natural assemblages of impression fossils on bedding planes in claystone. In this study, 13 assemblages of Hindeodus species were recognized, comprising at most 13 elements which generally maintain the original composition and structure of an apparatus. We discriminated pairs of carminiscaphate P1, angulate P2 and makellate M elements, as well as a single alate S0 element and two digyrate and four bipennate elements constituting the S array. Although the digyrate and bipennate elements are preserved in the S2 and S3–4 positions, respectively, a pair of S1 elements was not found due to incompleteness in the natural assemblages. The conodont biostratigraphy indicates that the lithological boundary between chert and claystone units in the study section corresponds exactly to the Permian–Triassic boundary.