The abundance, diversity and extinction of non-marine algae are controlled by changes in the physical and chemical environment and community structure of continental ecosystems. We review a range of non-marine algae commonly found within the Permian and Triassic strata of Gondwana and highlight and discuss the non-marine algal abundance anomalies recorded in the immediate aftermath of the end-Permian extinction interval (EPE; 252 Ma). We further review and contrast the marine and continental algal records of the global biotic crises within the Permian–Triassic interval. Specifically, we provide a case study of 17 species (in 13 genera) from the succession spanning the EPE in the Sydney Basin, eastern Australia. The affinities and ecological implications of these fossil-genera are summarised, and their global Permian–Triassic palaeogeographic and stratigraphic distributions are collated. Most of these fossil taxa have close extant algal relatives that are most common in freshwater, brackish or terrestrial conditions, and all have recognizable affinities to groups known to produce chemically stable biopolymers that favour their preservation over long geological intervals. However, these compounds (e.g., sporopollenin and algaenan) are not universal, so the fossil record is sparse for most algal groups, which hinders our understanding of their evolutionary histories. Owing partly to the high preservational potential of Zygnematophyceae, a clade of freshwater charophyte algae and sister group to land plants, this group has a particularly diverse and abundant Permian–Triassic fossil record in Gondwana. Finally, we review and contrast the marine and continental algal records of the global biotic crises within the Permian–Triassic interval. In continental settings, Permian algal assemblages were broadly uniform across most of southern and eastern Gondwana until the EPE; here, we propose the Peltacystia Microalgal Province to collectively describe these distinct and prolonged freshwater algal assemblages. In the immediate aftermath of the EPE, relative increases in non-marine algae have been consistently recorded, but the distributions of prominent taxa of Permian freshwater algae became severely contracted across Gondwana by the Early Triassic. We highlight the paucity of quantitative, high-resolution fossil evidence for this key group of primary producers during all biotic crises of the Permian and Triassic periods. This review provides a solid platform for further work interpreting abundance and diversity changes in non-marine algae across this pivotal interval in evolutionary history.