Lycophytes and ferns are spore-bearing vascular plants, and are important groups in the evolution history of land plants. With the progress of molecular systematic, the relationships of the major groups have been resolved, and the traditional concepts have been revised. Meanwhile, new systematic arrangements have been proposed and are continuously being revised and updated. In the present review, the most recent phylogenetic studies were discussed and a new classification system of the extant lycophytes and ferns from China was also proposed. The system comprises five subclasses, 14 orders, 39 families with 12 subfamilies, and about 140 genera of lycophytes and ferns distributed in China.