The fossil record of tubeworms is scarce compared to that of chemosynthetic bivalves although tubeworms are one of the dominant inhabitants among seep and vent faunas at present. This study reports tubeworm fossils observed on a float of muddy dolomite concretion from the Middle Miocene Bessho Formation, central Japan. Vesicomyid bivalve fossils with seep carbonates have been reported from many localities of the Bessho Formation. The concretion float contains abundant tubes, 1 to 4 mm in diameter, with no surface ornamentation and their inner space filled by chalcedony. In microscopic view, the tubes consist of flexible multi-layered organic sheets, over 100 µm thick, which were deformed and delaminated. The tubes gently curve and are unbranched, elongating in an almost same direction; they form aggregation patches, separated from each other in matrix-supported condition. The tube aggregate matrices are more calcareous than the muddy surroundings. The tube size, wall structure and aggregation in calcareous patches are similar to posterior ‘root’ tubes of vestimentiferans in present seep sites such as the Gulf of Mexico and Congo deep-sea fan. Our study represents the first fossil record of tubeworms from a dolomite concretion, suggesting that silicification could be an important factor for fossil preservation of flexible tubes against sub-bottom fluidization, deformation, and dissolution of initial calcium carbonates.