Many commentators argue that there is a flaw in Bayle’s plea for tolerance: the so-called “conscientious persecutor aporia.” In order to show the wrongness of persecutions, Bayle appeals to the primary ethical imperative of obeying the “dictates” of one’s conscience. It is wrong to oblige others to do something that their conscience judges to be bad because it obliges them to do something immoral. But if the integrity of conscience should always be respected, it seems that, as a consequence, one must not stop fanatics whose consciences order them to persecute dissenters. Therefore, Bayle’s theory appears to justify intolerance. However, I demonstrate that there actually is no “conscientious persecutor aporia.” The semblance of an aporia results from 1) a confusion between two steps of Bayle’s argument, and 2) errors in interpretation of his moral philosophy—specifically, the conditions for an action to be good and the nature of conscience.