The relationships among the extant five gymnosperm groups--gnetophytes, Pinaceae, non-Pinaceae conifers (cupressophytes), Ginkgo, and cycads--remain equivocal. To clarify this issue, we sequenced the chloroplast genomes (cpDNAs) from two cupressophytes, Cephalotaxus wilsoniana and Taiwania cryptomerioides, and 53 common chloroplast protein-coding genes from another three cupressophytes, Agathis dammara, Nageia nagi, and Sciadopitys verticillata, and a non-Cycadaceae cycad, Bowenia serrulata. Comparative analyses of 11 conifer cpDNAs revealed that Pinaceae and cupressophytes each lost a different copy of inverted repeats (IRs), which contrasts with the view that the same IR has been lost in all conifers. Based on our structural finding, the character of an IR loss no longer conflicts with the "gnepines" hypothesis (gnetophytes sister to Pinaceae). Chloroplast phylogenomic analyses of amino acid sequences recovered incongruent topologies using different tree-building methods; however, we demonstrated that high heterotachous genes (genes that have highly different rates in different lineages) contributed to the long-branch attraction (LBA) artifact, resulting in incongruence of phylogenomic estimates. Additionally, amino acid compositions appear more heterogeneous in high than low heterotachous genes among the five gymnosperm groups. Removal of high heterotachous genes alleviated the LBA artifact and yielded congruent and robust tree topologies in which gnetophytes and Pinaceae formed a sister clade to cupressophytes (the gnepines hypothesis) and Ginkgo clustered with cycads. Adding more cupressophyte taxa could not improve the accuracy of chloroplast phylogenomics for the five gymnosperm groups. In contrast, removal of high heterotachous genes from data sets is simple and can increase confidence in evaluating the phylogeny of gymnosperms.