Properties of semiconductors are largely defined by crystal imperfections including native defects. Van der Waals (vdW) semiconductors, a newly emerged class of materials, are no exception: defects exist even in the purest materials and strongly affect their electrical, optical, magnetic, catalytic and sensing properties. However, unlike conventional semiconductors where energy levels of defects are well documented, they are experimentally unknown in even the best studied vdW semiconductors, impeding the understanding and utilization of these materials. Here, we directly evaluate deep levels and their chemical trends in the bandgap of MoS2, WS2 and their alloys by transient spectroscopic study. One of the deep levels is found to follow the conduction band minimum of each host, attributed to the native sulfur vacancy. A switchable, DX center - like deep level has also been identified, whose energy lines up instead on a fixed level across different hosts, explaining a persistent photoconductivity above 400 K.