We present a genome assembly of Herbertus hutchinsiae (juniper prongwort; Streptophyta; Jungermanniopsida; Jungermanniales; Herbertaceae). The genome sequence has a total length of 1 091.90 megabases. Most of the assembly (99.56%) is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial sequence has a length of 161.56 kilobases and the plastid genome assembly has a length of 117.07 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.