The purpose of this paper is to clarify the reason of the difference in damage between Tofukuji Temple and Toji Temple in the 1596 Keicho-fushimi Earthquake. First, the differences of building damage at two temples are summarized. Next, we conduct microtremor measurements of the buildings and ground in two temples. These results reveal differences in amplification characteristics of ground motions due to the subsurface structure of the Kyoto basin. Therefore, we examine the differences in amplification characteristics of pulse-like ground motions and their consistency with the damage situation in the 1596 earthquake using two-dimensional ground models.