In the Bag-of-Words (BoW) model, the vocabulary is of key importance. Typically, multiple vocabularies are generated to correct quantization artifacts and improve recall. However, this routine is corrupted by vocabulary correlation, i.e., overlapping among different vocabularies. Vocabulary correlation leads to an over-counting of the indexed features in the overlapped area, or the intersection set, thus compromising the retrieval accuracy. In order to address the correlation problem while preserve the benefit of high recall, this paper proposes a Bayes merging approach to down-weight the indexed features in the intersection set. Through explicitly modeling the correlation problem in a probabilistic view, a joint similarity on both image- and feature-level is estimated for the indexed features in the intersection set. We evaluate our method on three benchmark datasets. Albeit simple, Bayes merging can be well applied in various merging tasks, and consistently improves the baselines on multi-vocabulary merging. Moreover, Bayes merging is efficient in terms of both time and memory cost, and yields competitive performance with the state-of-the-art methods.