Cell suspension culture has rapidly become an alternative source of taxol, an anticancer compound. To investigate the role of DNA methylation in the cultural course of Taxus chinensis cells, analyses of 18S rRNA gene sequences of cultured T. chinensis cells and related species were conducted. The phylogenetic analysis of 18S rRNA gene sequences indicated that HG-1 (the cultured T. chinensis cells), like T. mairei (the natural variety of T. chinensis), should be a new variety of T. chinensis, and cell culture can change the 18S rRNA gene sequence at the level of species despite 18S rRNA is the most conserved gene. The analyses of the CpG and TpG+CpA relative abundance and GC content of the 18S rRNA gene sequences made clear that DNA methylation contributed to changes of the 18S rRNA gene sequence of HG-1 at the level of species, which can make HG-1 to become a new variety of T. chinensis.