We investigated Permian strata in the Ota area of the Kosado Hills, Sado Island, central Japan, and their depositional ages were determined based on radiolarian biostratigraphy and zircon U–Pb dating. We also focused on the geology of the region and its lithologic correlation with other geological units in the Inner Zone of Southwest Japan. The radiolarian analysis identified the presence of Follicucullus porrectus and F. dilatatus in mudstone exposed on the coastline of Ota, indicating a middle–late Capitanian to early Changhsingian age. Mudstone exposed along the forest road in the Ota area contained Cariver charveti, suggesting a late Capitanian–early Changhsingian age. Zircon U–Pb dating of the tuff layer intercalated within the Follicucullus-bearing mudstone yielded a weighted-mean age of 259.9 ± 2.0 Ma, corresponding to a Capitanian–Wuchiapingian age. The tuffaceous sandstone interbedded with mudstone containing C. charveti yielded a weighted-mean age of 264.1 ± 6.3 Ma, which covers the Roadian to Wuchiapingian ages. The youngest model peak age (256.6 ± 2.6 Ma; Wuchiapingian) provides the most reliable estimate of the maximum depositional age. The Paleozoic strata in the Kosado Hills have previously been correlated with the Ultra-Tamba and Maizuru belts in Southwest Japan based on fossil occurrences. Our findings indicate that the Permian rocks in the Kosado Hills exhibit differences in lithology from those in the Ultra-Tamba belt but share similarities with the upper Guadalupian–Lopingian strata in the Maizuru belt.