Transcription factor/Translation factor (TF) play a central role in gene regulation. Knowing the binding specificities of TFs is essential for developing models of the regulatory processes in biological systems and for deciphering the mechanism of gene expression. In this talk, I will first present the fundamental issue for motif prediction of biological sequences, then systematically present motif prediction of biological sequences in combination with the popular emerging technology “Deep Neural Networks”. Firstly, several classical models for deep neural network and the research status of biological sequence motif prediction will be briefly introduced, and the existing shortcomings of deep-learning based motif prediction is discussed, some motif prediction methods including high-order convolutional neural network architecture, weakly-supervised convolutional neural network architecture, deep-learning based sequence + shape framework and bidirectional recurrent neural network for DNA motif prediction are briefly overviewed. Secondly, some latest results are importantly presented. Finally, some new research problems in this aspect will be pointed out and over-reviewed.