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Background  Phylogenetic relationships among Eastern Hemisphere cypresses, Western Hemisphere cypresses, junipers, and their closest relatives are controversial, and generic delimitations have been in flux for the past decade. To address relationships and attempt to produce a more robust classification, we sequenced 11 new plastid genomes (plastomes) from the five variously described genera in this complex ( Callitropsis ,  Cupressus ,  Hesperocyparis ,  Juniperus , and  Xanthocyparis ) and compared them with additional plastomes from diverse members of Cupressaceae.    Results  Phylogenetic analysis of protein-coding genes recovered a topology in which  Juniperus  is sister to  Cupressus , whereas a tree based on whole plastomes indicated that the  Callitropsis - Hesperocyparis - Xanthocyparis  (CaHX) clade is sister to  Cupressus . A sliding window analysis of site-specific phylogenetic support identified a ~ 15 kb region, spanning the genes  ycf1  and  ycf2 , which harbored an anomalous signal relative to the rest of the genome. After excluding these genes, trees based on the remainder of the genes and genome consistently recovered a topology grouping the CaHX clade and  Cupressus  with strong bootstrap support. In contrast, trees based on the  ycf1  and  ycf2  region strongly supported a sister relationship between  Cupressus  and  Juniperus .    Conclusions  These results demonstrate that standard phylogenomic analyses can result in strongly supported but conflicting trees. We suggest that the conflicting plastomic signals result from an ancient introgression event involving  ycf1  and  ycf2  that occurred in an ancestor of this species complex. The introgression event was facilitated by plastomic recombination in an ancestral heteroplasmic individual carrying distinct plastid haplotypes, offering further evidence that recombination occurs between plastomes. Finally, we provide strong support for previous proposals to recognize five genera in this species complex:  Callitropsis ,  Cupressus ,  Hesperocyparis ,  Juniperus , and  Xanthocyparis .    Electronic supplementary material  The online version of this article (10.1186/s12862-018-1258-2) contains supplementary material, which is available to authorized users.

Phylogenomic evidence for ancient recombination between plastid genomes of the Cupressus-Juniperus-Xanthocyparis complex (Cupressaceae)