© 2017 The Author(s). To evaluate local site effects in Kumamoto City, we installed six temporary seismic stations along a 6-km north-south survey line in the city immediately after the 2016 Kumamoto earthquake foreshock (Mj 6.4), which occurred on April 14, 2016. Seismic data from the 2016 Kumamoto earthquake (Mj 7.3), which occurred on April 16, 2016, were successfully recorded at two sites and indicated large amplitudes in the frequency range of 0.5-3 Hz. Site amplifications estimated from weak ground motion data, with a station at Mt. Kinbo used as a reference, are relatively variable along this survey line; however, site amplification factors in the frequency range of 0.5-3 Hz are not large enough to explain the amplitudes produced by the main shock. Nevertheless, site amplifications estimated from strong ground motion data recorded at the two sites during the main shock are large in the frequency range of 1-3 Hz. These findings reveal that the strong ground motions in the frequency range of 1-3 Hz were enhanced by nonlinear behavior of the subsurface soil in Kumamoto City. Moreover, it is observed that the frequency contents of the main shock data in the frequency range of 0.7-3 Hz differ significantly between the two sites, despite the proximity of these sites (600-m interval). Therefore, we also performed single-station microtremor measurements with an interval distance of approximately 100 m between these two sites. We confirmed that the peak frequencies of the horizontal-to-vertical spectral ratios of microtremors have trends that are similar to those of the site amplification factors between the two sites. However, these results could not explain the differences in strong ground motions observed at the two sites during the 2016 Kumamoto earthquake.[Figure not available: see fulltext.]