Chloroplast DNAs (cpDNAs) of conifers and Gnetales share aspects of gene organization absent from angiosperm cpDNAs. The distribution of these similarities is intriguing as it conflicts with the widely-held view of Gnetales as the sister-group of angiosperms. However several recent studies by other workers also have called this paradigm into question. These other analyses have supported the gymnosperms as a monophyletic clade or have supported, specifically, a Gnetales-conifer clade. The cpDNA gene organization provides additional support for a conifer-Gnetales relationship. One cpDNA similarity shared between conifers and Gnetales (but lacking in angiosperms cpDNAs) is the duplication (partial in the case of conifers; complete in Gnetales) of the psbA gene. In addition, a duplication of the trnI gene is found between trnH and psbA only in the cpDNAs of conifers and Gnetales. These shared structural similarities appear to be homologous and derived. Other possible structural similarities are currently under investigation and may be discussed.

Key words: conifers, cpDNA, Gnetales, phylogeny, structural mutation