Permian-Triassic boundary problems in the Tsukumi Limestone, Southern Chichibu Terrane, SW Japan, have been of special interest since the discovery in this unit of the latest Permian fusuline genus “Palaeofusulina” and Early Triassic bivalves about 40 years ago. This paper shows that the Upper Permian (Lopingian) part of the Tsukumi Limestone is 1) strongly fractured as a whole, 2) more or less dolomitized and recrystallized, 3) tectonically interposed by Middle Permian (Capitanian) limestone wedges, and 4) in fault contact with probable Triassic carbonates. The Late Permian foraminiferal fauna consists of 37 taxa, of which six genera and seven species are fusulines, including the new staffellid genus and species, Tsukumiella tsukumiensis. Samples with Codonofusiella kwangsiana are assigned with certainty to the Wuchiapingian, whereas others without this species are of indeterminate Wuchiapingian or Changhsingian age. Although Palaeofusulina was not found, the Tsukumi contains the first known occurrence of Colaniella from Permian limestone imbedded in Jurassic–Cretaceous terranes of the circum-Pacific. The Late Permian foraminiferal fauna of the Tsukumi Limestone is paleobiogeographically and tectonically important for understanding the faunal provincialism and plate movement of continental and seamount limestone blocks in the Late Permian, along with the coeval faunas of the Takachiho and Shirokawa-Nomura areas in SW Japan.