In the post-genomic era after human whole-genome sequencing has been completed, accurate functional annotation of genomic sequences, especially the DNA regulatory elements, has become an urgent need of further in-depth understanding of the complex mechanisms of human genome. Recent large-scale chromatin states mapping efforts have revealed characteristic chromatin modification signatures for various types of functional DNA elements. The conclusions drew in these studies have promoted the emergence of a series of supervised and unsupervised methods of DNA elements identification, some of which have been successfully applied to identify functional DNA elements in a number of genomes and have become the regular tools to decode an unknown genome. These methods are adept at different aspects of genomic studies, varied by the embedded algorithms and the identification strategies. In most cases users should consider joint application of different types of methods to obtain a balance between identification sensitivity and specificity. Despite the successful applications of current methods, each type of methods has its own disadvantages which users should scrupulously avoid. In this paper, we not only reviewed the main types of previous and current DNA elements identification methods, and comprehensively analyzed the advantages and disadvantages of each type of methods, but also pointed out the next possible directions of method improvement. We anticipated the analysis and views put forward in this review could help readers to deepen the understanding of principles of DNA elements identification methods, thus better applied them in their own studies.