Abstract We have examined the phylogenetic distribution of a rare structural mutation in the chloroplast genome of conifers. An exception to the otherwise highly conserved basic structure of land plant chloroplast-DNA (cpDNA) was reported previously in two species of the conifer family Pinacease, where one copy of the inverted repeat was shown to be absent. The present study examined a broad taxonomic representation of conifers, including at least one member of each family, plus representatives of each of the other major extant vascular plant lineages. Our results indicate only one copy of the “repeat” is present in all conifers, whereas two copies were found in those pteridophytes and non-coniferous seed plants surveyed. The evidence that the loss is shared throughout the conifers but with none of the extent outgroups strongly supports conifer monophyly.