For a finite group $G$ of Lie type and a prime $p$, the authors compare the automorphism groups of the fusion and linking systems of $G$ at $p$ with the automorphism group of $G$ itself. When $p$ is the defining characteristic of $G$, they are all isomorphic, with a very short list of exceptions. When $p$ is different from the defining characteristic, the situation is much more complex but can always be reduced to a case where the natural map from...