Sequences of the nuclear gene 18s rRNA, chloroplast genes rbcL, matK, rps4 and mitochondrial gene cox Ⅰ from 32 species of the families Taxaceae, Podocarpaceae, Cephalotaxaceae, Pinaceae, Taxodiaceae, Cupressaceae, Sciadopityaceae, Phyllocladaceae and Araucariaceae, with the genera Abies and Pinus as outgroups were analyzed using maximum parsimony, neighbor joining and maximum likelihood methods to reconstruct the phylogenetic relationships of Taxaceae. The combined analysis strongly supported that Taxus, Pseudotaxus, Amnentotaxus, and Torreya comprise a monophyletic group, among which two clades, TorreyalAmentotaxus and Taxus Ⅰ Pseudotaxus, are resolved. The combined analysis indicate that Cephalotaxaceae and Taxaceae form a mnonophyletic group, with the Taxodiaceae Ⅰ Cupressaceae clade as their sister group. Sciadopityaceae is sister to clade of Taxodiaceae, Cupressaceae, Cephalotaxaceae and Taxaceae. The four genera of Podocarpaceae comprise a monophyletic group. Phyllocladaceae is sister to Podocarpaceae, and Araucariaceae is sister to monophyletic Phyllocladaceae Ⅰ Podocarpaceae clade.