Label-free biosensors (LFBs) have demonstrated a great potential in cost-effective applications, and most of the DNA-based LFBs are based on the principle of binding-induced structural transformation. This review is a collection of the latest reported studies, which have employed structure-selective nucleic acid dyes for the development of DNA-based LFBs. The collections in this review have been structured based on the selective binding of dyes towards specific DNA conformations, including single-stranded DNA, double-stranded DNA, triplex DNA, i-motifs and G-quadruplexes. The newest studies of employing versatile nucleases, fascinating nanomaterials, logic gates and cascades, DNA junctions and nanostructures have also been collected as examples. It is predicted that the imperative requirement for ultrahigh sensitivity, intelligent analysis, reliable detection, portable and fast assay would force the LFB development in a stimulative and continuous way.