Abstract In order to understand the phylogenetic relationships among Cupressaceae species, we investigated phylogenetic relationships of nine species from four subfamilies Cupressoidae, Taxodioidae, Cunninghamioidae and Taiwanioidae using 18S ribosomal DNA sequences. DNA total was extracted from young leaves or inner barks of 5 species: Cunninghamia lanceolata var. konishii, Xanthocyparis vietnamensis, Cupressus tonkinensis, Calocedrus macrolepis and Fokienia hodginsii. Variable nucleotide from the studies together with the 4 species reported in GenBank was used to contruct a phylpgenetic trees. The analyses indicated two lineages, i.e. Taiwanioidae/Cunninghamioidae contains the species in genera Cunninghamia and Taiwania, and Cupressoidae/Taxodioidae contains the species in the six remaining genera Cupressus, Calocedrus, Fokienia, Xanthocyparis, Juniperus and Crytomeria. Within the Cupressoidae, Xanthocyparis is strongly associated with Cupressus, and sharing a sister relationship with Juniperus. The data also indicated that Cunninghamia clusters with Taiwania.