A phylogenetic sequence in the radiolarian genus Albaillella, from Changhsingian chert sequences of Upper Permian, Upper Ubara, Gochi-Hachawa, and Tenjinmaru, Southwest Japan, is divided into six lineage-zones. The youngest two of these zones are new, and are based on newly recognized dwarfed taxa in depauperate faunas. Conodont correlations between the Japanese sections and the Permo-Triassic GSSP at Meishan, southern China, is strengthened by new end-Permian pelagic conodont biozonation from Huangshi, Hubei, China. The correlations show that the decline and extinction of the albaillellinid lineage coincides with the period of mass extinction at the end of the Permian. The two depauperate Albaillella lineage-zones alternate with three barren interzones with anomalous isotope ratios, supporting the theory that the end-Permian event may actually have consisted of three closely-spaced biotic crises; a fourth crisis is suggested in basal Triassic strata at Huangshi. Because the deep-water radiolarian lineage can be closely correlated with the Permo-Triassic GSSP utilizing conodonts, most notably by the boundary-index conodont Hindeodus parvus (Kozur and Pjatakova), we suggest that the Ubara section may be a good candidate for a boundary hypostratotype section in a pelagic cherty facies in which planktonic fossils are abundantly preserved, and in which the Permo–Triassic boundary may be confidently correlated.