The carbon (δ13Corg) and nitrogen (δ15N) isotopic compositions of bulk organic matter were analyzed in two high-resolution Permian-Triassic transitional sections containing microbialite in south China. The results from these shallow-marine sections show that an abrupt negative shift in δ15N, from ∼+3‰ to ∼0‰, occurred immediately after the latest Permian mass extinction (LPE) in both sections, concurrent with a distinct negative shift in δ13Corg. The persistently low values of δ15N suggest that, following the LPE, microbial nitrogen fixation became the main source of biologically available nitrogen in the Nanpanjiang Basin and perhaps over a broader region of the eastern Paleotethys Ocean. Enhanced N fixation is probably indicative of the prevalence of stratified anoxic water masses characterized by intense denitrification and/or anaerobic ammonium oxidation at the time. Perturbation of the marine nitrogen cycle might have contributed to high temperatures following the main marine mass extinction through the release of the greenhouse gas N2O. The sharp declines in δ15N and δ13Corg may be ascribed to an abrupt change in shallow-water microbial communities, which differed in composition from contemporaneous deep-water communities.