We present the first study of micro-crustaceans (ostracods) associated with microbial crusts in the aftermath of the most devastating extinction, the end-Permian extinction (EPE). These post-extinction microbialites dominated shallow shelf marine environments and were traditionally considered as devoid of any associated fauna. We present a micro-palaeontological analysis of a large record from microbial and non-microbial settings following the EPE. This dataset documents the proliferation of ostracods strictly associated with microbialites. Based on the diet of extant ostracods and uniformitarianism, we propose that the abundant microbes in the mats served as an unlimited food supply. Photosynthetic cyanobacteria may also have locally provided oxygen under low oxygen conditions interpreted by others for the microbialites. Microbialites provided a specialised environment that may have acted as refuge for ostracods in the immediate aftermath of the EPE. The surviving faunas may have been progenitors for the starting of the latter radiation.