There are several theories, including the possibility of a meterorite hitting the planet. Previously, most researchers believed that the Permian mass extinction was a result of a series of volcanic eruptions in what is now Siberia. These eruptions would have caused a dramatic rise in the amount of greenhouse gases which would have, in turn, killed off a bulk of species.
However, Daniel Rothman from the Massachusetts Institute of Technology is floating around a different theory. As he presented in a meeting for the American Geophysical Union, he believes that the mass extinction could have been caused by something much smaller. His theory is that the extinction was caused by a single strain of bacteria.