Before molecular tools were available, the oldest extant conifer groups were postulated to be the Pinaceae, Podocarpaceae/Phyllocladaceae and Araucariaceae, but their exact relationships were unclear. Recent molecular evidence from chloroplast and nuclear genomes (rbcL and 18S rRNA) supports this hypothesis and clarifies the relationships among the derived conifers, the Taxaceae, Cephalotaxaceae and Cupressaceae s.l. We introduce sequences of the slowly-evolving mitochondrial gene, coxI, from every family of extant gymnosperms, including three families of cycads, Ginkgo, the three gnetophyte genera and all conifer families. coxI sequences have a low fundamental (synonymous) rate of base substitution and yield parsimony trees which are predictably lower in homoplasy (C.I. = 0.6238) than either rbcL (C.I. = .4310) or 18S rRNA (C.I. = .4821). Most informative characters in the coxI data set change only once or twice across the whole tree while a much larger fraction of characters in the other data sets change three or more times. T to C transitions contribute most of the variation at first and second positions and are probably the result of a high level of RNA editing in conifers -- editing allows "synonymous" base substitutions in the DNA that are corrected during mRNA processing. Because of potential editing differences among gymnosperm families, sequences are analyzed both with and without editing sites. At the base of the conifers is the Pinaceae, and then the Podocarpaceae and Phyllocladaceae form a clade sister to the rest of the conifers. Phyllocladus is well-supported as a member of the Podocarpaceae, but Sciadopitys is distinctly outside of the Cupressaceae clade, and should probably be kept in its monotypic family, the Sciadopityaceae. The Taxaceae, Cephalotaxaceae and Cupressaceae form a highly supported clade in coxI trees just as in rbcL and 18S rRNA trees.

Key words: conifers, coxI, gymnosperms, mitochondrial DNA, molecular evolution, molecular phylogeny