Microstructural elements of Permian-Triassic boundary limestones from localities Idrijca and Masore in northwestern Slovenia are investigated. These microstructural elements prove microbial origin of investigated limestones. Permian-Triassic microbial limestones from Slovenia are compared with similar deposits from China and Hungary of the same age. Localities in Slovenia, as well as in Hungary and China, represent marginal parts of Paleotethys with sedimentation on carbonate platforms and ramps. After end-Permian mass extinction, microbial communities dominated and formed carbonate microbial crusts. Microbial carbonate crust precipitation was driven by Ca-bicarbonate rich (sometimes anoxic) waters that upwelled from the deep ocean and enhanced calcium carbonate precipitation in the shallow part of the ocean, on the shelf. In microbial precipitates, microstructural elements that prove that microbial origin are differentiated as: spheres and sphere clusters, bushy aggregates of micrite clots, prostrate micrite threads and peloids. Spheres represent remains of calcified coccoidal cyanobacteria. Elongate microstructures are defined as prostrate micrite threads. Bushy agregates of micrite clots also has microbial origin. Adachi et al. (2004) explained microbial origin of some peloids. Beside those four elements, Kershaw et al. (1999) noted microspheres - spherical carbonate depositional objects with dark micrite rim and sparitic nuclei. He interpreted that some microspheres originated from the fossils (mainly ostracods), but in this investigation in some samples from Idrijca it is proved that microspheres are detrital objects and that they can be at least partly formed by microbs.