The occurrence of large earthquakes and tsunamis along the Ryukyu Trench is a subject of continuing interest, the key to which is the long-term geological record. Here we describe the clast size and spatial distributions of ∼2900 boulders on the reefs of the Ryukyu Islands, Japan, as markers of paleotsunamis and causative tsunamigenic earthquakes. Boulders of tsunami origin were observed only at a specific island group at the southern end, suggesting the local occurrence of tsunamigenic earthquakes there. In contrast, in the central to northern Ryukyu Islands, no evidence exists of tsunamis larger than those at the southern end of the Ryukyu Islands during the past 2000–3000 yr. These islands have numerous boulders deposited by storm waves during the past 2300 yr or earlier. Their spatial distribution has not been disturbed by large tsunamis. This suggests that large tsunamis did not strike this area during that period; nevertheless, these regions are seismically active. Our study shows that coastal boulder deposits present great potential to not only ascertain the histories and effects of paleotsunamis but also to constrain fault models of the causative earthquakes.