The end of the Permian Period was marked by the most severe mass extinction in the geologic record. Detailed quantitative study of pollen and spores from shallow-marine deposits spanning the Permian-Triassic (P-Tr) boundary in Israel reveals a sequence of palynological-ecological stages reflecting a major crisis among land plants. The disappearance of the gymnosperm-dominated palynoflora of the Late Permian Lueckisporites virkkiae Zone is recorded at a claystone horizon containing almost exclusively abundant fungal remains and carbonized terrestrial plant debris. This “fungal spike” is followed by a zone dominated by marine acritarchs and a succession showing ecological recovery with abundant lycopod spores and eventual reappearance of bisaccate gymnosperm pollen in the Early Triassic. The latest Permian proliferation of fungi is recognizable worldwide and can be correlated with other paleontological and geochemical markers of a global ecological disaster.