Hornworts are a bryophyte lineage that diverged from other extant land plants >400 million years ago and bear unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis, and pyrenoid-based carbon-concentrating mechanism (CCM). Here we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses placed hornworts sister to liverworts+mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomata function are conserved in Anthoceros and up-regulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis, and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants.