In situ fossil barnacle populations (Cirripedia, Balanomorpha) are described from the Miocene Natori Group of the Moniwa-Goishi area, northeast Japan. The Natori Group exhibits a transgressive sequence from subaerial lavas and volcaniclastics (Takadate Formation) to shoreface-shelf deposits (Moniwa and Hatatate formations) in ascending order. In the Takadate Formation, volcaniclastics locally intercalate bay deposits in which the fossil barnacle Balanus bisulcatus occurs on gravel surfaces in situ. The Takadate Formation is unconformably overlain by the basal conglomerate of the Moniwa Formation, which is interpreted as a ravinement deposit formed in an open coast. An extinct barnacle species, Concavus sendaicus, is found as gregarious clusters and solitary individuals on boulder surfaces in the basal conglomerate in situ. These features suggest that B. bisulcatus inhabited in bay environments at the early transgressive stage. On the other hand, C. sendaicus was distributed over open-coast environments during subsequent marine flooding. The in situ C. sendaicus provides strong evidence for the reconstruction of the extinct species habitat.