Previous work indicates that a variety of microbes bloomed in the oceans after the end-Permian faunal mass extinction, but evidence is sporadically documented. Thus, the nature and geographic distribution of such microbes and their associations are unclear, addressed in this study using a series of biomarker groups. On the basis of microbial biomarker records of the 2-methylhopane index, evidence is presented for cyanobacterial blooms in both the western and eastern Tethys Sea and in both shallow and deep waters, after the mass extinction. The enhanced relative abundance of C28 (expressed by the C28/C29 ratio of) regular steranes suggests a bloom of prasinophyte algae occurred immediately after the end-Permian faunal extinction, comparable with those observed in some other mass extinctions in Phanerozoic. Significantly, cyanobacteria and prasinophyte algae show a synchronized onset of bloom in the shallow water Bulla section, north Italy, inferring for the first time their coupled response to the biotic crisis and the associated environmental conditions. However, in Meishan of Zhejiang Province in south China, the bloom declined earlier than in Bulla. The association of increased 2-methylhopane index with a negative shift in the nitrogen isotope composition infers a scenario of enhanced nitrogen fixation by cyanobacteria immediately after the faunal mass extinction. N2 fixation by cyanobacteria is here interpreted to have provided prasinophyte algae with ammonium in nutrient-limited shallow waters, and thus caused their associated blooms.