Abstract: DNA sequences, because of their disparity in rate of evolution, are suitable for phylogenetic study at different taxonomic levels. Therefore, selecting the most appropriate DNA sequence to address a certain phylogenetic issue is impor-tant. This paper summarizes the appropriate range of some DNA sequences that are commonly used in current pteridophyte molecular phylogenetics, which comprises sequences from three plant genomes (chloroplast, nucleo-tide, and mitochondria), especially focuses on the usage of chloroplast DNA regions. Problems in reconstructing the fern phylogeny and strategies to overcome these problems (including ingroup and outgroup selection, and the choice of the appropriate DNA region) are briefly discussed. This paper re-presents recent progress in molecular phylogenetics and points out the status of and prospects for pteridological research in China.