The botanical history of gymnosperm classification was reviewed and dividied into six major phases since the initiation of modern taxonomy in 1753 according to landmark concepts or creative classifications. The first phase lasted from Linnaeus to Brown during which the concept of gymnosperm was not conceived, and gymnosperms were not treated as a taxon. This phase was represented by the sexual system of Linnaeus. The second phase was from Brown to Brongniart. In this phase, the concept of gymnosperms was proposed and gradually accepted by botanists at that time, and Brongniart treated gymnosperms as a group in his classification system though the linear sequence, family delineation and relationships among taxa were ambiguous. The third phase was from Brongniart to Braun. In this phase, the gymnosperms were treated as a group within dicotyledons, the classification of Bentham & Hooker was considered as the representative classification systems. The fourth phase was from Braun to Pilger. During this period, the gymnosperms were treated as a separate taxon from angiosperms, the spermatozoids of cycads and ginkgo were discovered, the main lineages of gymnosperms became established, but the family delineation remains ambiguous, representative systems include Eichler and Engler. The fifth phase was from Pilger to Christenhusz et al.. Numerous classifications of gymnosperms were proposed in this phase, various categories were applied to lineages of gymnosperms, different lines of evidence were obtained and utilized including morphology, anatomy, embryology, phytochemistry, palaeobotany, cladistics, the focuses of debates were mainly on the relationships and systematic positions of ginkgo, taxads, and gnetophytes, and the taxonomic delineation of Podocarpaceae, Taxodiaceae and Cupressaceae, the classification systems of Pilger and Wanchun Cheng were representative in this phase. The sixth phase was from Anderson et al. till now. In this phase, people accepted the principles of cladistics, and conducted phylogenetic studies using DNA sequences, and also integrated different lines of evidences in taxonomy. The new classification of gymnosperms proposed by Yang et al. was introduced and the features of this new classification was discussed. Future studies should focus on species delimitation based on Genomic barcoding, integrative taxonomy, and conservation biology.