Abstract: Batrachospermales are the largest group of freshwater red algae. Recently, DNA sequence analysis has been widely used in molecular systematics of Batrachospermales and offers a new path for phylogenetics study combined with traditionally morphological and ecological methods. This paper reviews the foundation of Batrachospermales and the groups included, then summarizes the molecular markers commonly applied for the study of the phylogeny and evolution of Batrachospermales. The algae show 18S rDNA, 26S rDNA and an internal transcribed spacer (ITS) region in the nuclear genome, an rbcL sequence in chloroplast DNA, and a cox2-3 spacer in mitochondrial DNA. Also discussed is the new technique of inter simple sequence repeat (ISSR) and the expansion of the applicable range of each molecular marker. The ITS region is mainly used for population differentiation and genetic analysis among closely related species, and ISSR is applicable for studying genetic diversity of interpopulations and individual variation. As well, the cox2-3 spacer is sometimes used for investigating genetic diversity of individual variation, whereas the rbcL sequence and 18S rDNA could be used for molecular studies at interspecific and higher taxonomic levels. These markers have been shown in phylogeography, dispersal mechanisms and the origin of species. The authors introduce the latest progress in this area and discuss the prospects for future research.