We introduce a novel Bayesian approach for deciphering complex substitution ciphers. Our method uses a decipherment model which combines information from letter n-gram language models as well as word dictionaries. Bayesian inference is performed on our model using an efficient sampling technique. We evaluate the quality of the Bayesian decipherment output on simple and homophonic letter substitution ciphers and show that unlike a previous approach, our method consistently produces almost 100% accurate decipherments. The new method can be applied on more complex substitution ciphers and we demonstrate its utility by cracking the famous Zodiac-408 cipher in a fully automated fashion, which has never been done before.