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PremisePhylogenetic trees of bryophytes provide important evolutionary context for land plants. However, published inferences of overall embryophyte relationships vary considerably. We performed phylogenomic analyses of bryophytes and relatives using both mitochondrial and plastid gene sets, and investigated bryophyte plastome evolution. MethodsWe employed diverse likelihood‐based analyses to infer large‐scale bryophyte phylogeny for mitochondrial and plastid data sets. We tested for changes in purifying selection in plastid genes of a mycoheterotrophic liverwort (Aneura mirabilis) and a putatively mycoheterotrophic moss (Buxbaumia), and compared 15 bryophyte plastomes for major structural rearrangements. ResultsOverall land‐plant relationships conflict across analyses, generally weakly. However, an underlying (unrooted) four‐taxon tree is consistent across most analyses and published studies. Despite gene coverage patchiness, relationships within mosses, liverworts, and hornworts are largely congruent with previous studies, with plastid results generally better supported. Exclusion ofRNAedit sites restores cases of unexpected non‐monophyly to monophyly forTakakiaand two hornwort genera. Relaxed purifying selection affects multiple plastid genes in mycoheterotrophicAneurabut notBuxbaumia. Plastid genome structure is nearly invariant across bryophytes, but thetufA locus, presumed lost in embryophytes, is unexpectedly retained in several mosses. ConclusionsA common unrooted tree underlies embryophyte phylogeny, [(liverworts, mosses), (hornworts, vascular plants)]; rooting inconsistency across studies likely reflects substantial distance to algal outgroups. Analyses combining genomic and transcriptomic data may be misled locally for heavilyRNA‐edited taxa. TheBuxbaumiaplastome lacks hallmarks of relaxed selection found in mycoheterotrophicAneura. Autotrophic bryophyte plastomes, includingBuxbaumia, hardly vary in overall structure.