Stable isotopes of inorganic and organic carbon are commonly used in chemostratigraphy to correlate marine and terrestrial sedimentary sequences based on the assumption that the carbon isotopic signature of the exogenic carbon pool dominates other sources of variability. Here, sediment samples from four Permian–Triassic boundary (PTB) sections of western Guizhou and eastern Yunnan provinces in South China, representing a terrestrial to marine transitional setting, were analyzed for δ¹³C of organic matter (δ¹³C_org). These values were subsequently compared to published δ¹³C values of carbonates (δ¹³C_carb) from the Global Stratotype Section and Point at Meishan and many other marine and terrestrial sections. A similar isotopic trend evident through all four sections is characterized by a negative shift of 2–3‰ at the top of the Xuanwei Formation, where we tentatively place the PTB. This negative shift also corresponds to a turnover in the vegetation and the occurrence of fungal spores, which is generally interpreted as a proliferation of decomposers and collapse of complex ecosystems during the end-Permian mass extinction event. Moreover, the absolute values of δ¹³C_org are more extreme in the more distal (marine) deposits. The δ¹³C_org values for the studied sediments are more variable compared to coeval δ¹³C_carb records from marine records especially in the interval below the extinction horizon. We contend that the depositional environment influenced the δ¹³C_org values, but that the persisting geographic δ¹³C_org pattern through the extinction event across the four independent sections is an indication that the atmospheric δ¹³C signal left an indelible imprint on the geologic record related to the profound ecosystem change during the end-Permian extinction event.