N6-methyladenosine (m6A), as one of the most well-studied RNA modifications, has been found to be involved with a wide range of biological processes. Recently, diverse computational methods have been developed for automated identification of m6A sites within RNAs. To identify m6A sites accurately, one of the major challenges is to extract informative features to describe characteristics of m6A sites. However, existing feature representation methods are usually hand-crafted based, and cannot capture discriminative information of m6A sites. In this paper, we develop a m6A site predictor, named DeepM6APred. In this predictor, we propose to use a deep learning based feature descriptor with deep belief network (DBN) to extract high-level latent features. By integrating the deep features with traditional handcrafted features, we train a classification model based on support vector machine and successfully improve the predictive ability of m6A sites. Experimental results on a benchmark dataset show that our proposed method outperforms the state-of-the-art predictors, at least 2% higher in terms of Matthew’s correlation coefficient (MCC). Moreover, a webserver that implements the DeepM6APred is established, which is currently available at the website http //server.malab.cn/DeepM6APred. It is expected to be a useful tool to assist biologists to reveal the functional mechanisms of m6A sites.