The taxonomic classification of the genus Anadara (Bivalvia) from the Miocene Kubota Formation in the eastern Tanagura area has been controversial in previous studies, because there are wide ranges in its shell variation. The present study conducts morphometric analyses of fossil Anadara collected from three localities (Kamitoyo, Kubota, and Tanaka) of the formation as a basic study to describe the morphologic variation through time and space. As a result, the Kamitoyo population can be distinguished from other two populations by its shell shape and ontogenetic pattern. In turn, morphometric differences between Kubota and Tanaka populations should be resulted from an intraspecific variation because these two populations have a common ontogenetic pattern of the shell-coiling mode. According to ontogenetic parameters of hinge teeth, these three populations are placed in the subgenus Anadara. We distinguish the Kamitoyo population into an independent species Anadara (Anadara) tanakuraensis Noda from the rest two populations belonging to Anadara (Anadara) hataii Noda.