Expression of the eukaryotic genome is a highly complex and tightly regulated process, and its regulation depends on interactions among cis-acting elements and transcription factors. Identification of active gene regulatory elements is key to understanding transcriptional control of biological processes including differentiation, development, proliferation, cell-type specificity, and responses to the environment. DNase I hypersensitive sites (DHSs) are markers of open chromatin that provide a very effective method of targeting all types of cis-regulatory elements (CREs) including enhancers, promoters, insulators, silencers, and locus control regions. With the rapid development of sequencing technologies, many genomes have been sequenced. Identification of DHSs provides the potential for further animal functional genomics research. This review reveals recent advances in the identification and analysis of DHSs in animal genomes.