The Capitanian (late Guadalupian) high positive plateau interval of carbonate carbon isotope ratio (δ 13C carb) was recognized lately in a mid-Panthalassan paleo-atoll limestone in Japan as the Kamura event. This unique episode in the late-middle Permian indicates high productivity in the low-latitude superocean likely coupled with resultant global cooling. This event ended shortly before the Guadalupian–Lopingian (middle-late Permian) boundary (ca. 260 Ma); however, its onset time has not been ascertained previously. Through a further analysis of the Wordian (middle Guadalupian) to lower Capitanian interval in the same limestone at Kamura in Kyushu, we have found that the δ 13C carb values started to rise over +4.5‰ and reached the maximum of +7.0‰ within the Yabeina (fusuline) Zone of the early-middle Capitanian. Thus the total duration of the Kamura event is estimated over 3–4 million years, given the whole Capitanian ranging for 5.4 million years. This 3–4 million years long unique cooling event occurred clearly after the Gondwana glaciation period (late Carboniferous to early Permian) in the middle of the long-term warming trend toward the Mesozoic. This cooling may have been a direct cause of the end-Guadalupian extinction of low-latitude, warm-water adapted fauna including the large fusulines (Verbeekinidae), gigantic bivalves (Alatoconchidae), and rugose corals (Waagenophyllidae). The Kamura event marks the first sharp excursion of δ 13C carb values in the volatile fluctuation interval that lasted for nearly 20 million years from the late-Middle Permian until the early-Middle Triassic. This interval with high volatility in δ 13C carb values represents the transition of major climate mode from the late Paleozoic icehouse to the Mesozoic–Cenozoic greenhouse regime. The end-Paleozoic double-phased extinction occurred within this interval and the Capitanian Kamura event is regarded as the prelude to this transition.