We conducted array measurements of microtremors at six sites in and around the Sendai basin to estimate deep S-wave velocity structures above the seismological bedrock (pre-Tertiary bedrock). After estimating phase velocities of microtremors in the frequency range from about 0.5 to 3 Hz, we succeeded to estimate the deep structures above the pre-Tertiary bedrock at four soil sites (KATA, OKIN, ARAH, and MYG15) and only the upper part just beneath the Pliocene layer at the other soil site (TRMA) using a Rayleigh-wave inversion technique. At TRMA and a rock site TAMA, we roughly estimate the deep S-wave velocity structures using empirical site amplification factors derived from strong-motion records. The deepest bedrock depth is 1 km, and the shallowest depth is 200 m among these six sites. The difference of the bedrock depth between the eastern side and the western side of an active thrust fault, the Nagamachi-Rifu line, is only 120 m. The difference of the bedrock depth between two sites in the east of the basin reaches about 500 m, although any geological boundaries or buried faults have not been mapped. Since the deep S-wave velocity structure of the Sendai basin had been basically unknown, we delineate it for the first time in this article using array measurement of microtremors.