Leonurus japonicusHoutt. is an important medicinal plant in East Asia and is now widely recognized for its role in treating cerebral apoplexy and lowering blood lipids. Here, we report two sets of chromosome-level genome sequences for leonurine-producingLeonurus japonicusand for its closely related species leonurine-freeLeonurus sibiricus, where 99.78% of 518.19 Mb ofL. japonicuswas assembled into ten pseudochromosomes with a contig N50 of 17.62 Mb and 99.33% of 472.29 Mb ofL. sibiricuswas assembled into nine pseudochromosomes with a contig N50 of 13.29 MB. The reference genomes ofLeonuruswill accelerate the decoding of novel bioactive molecules in medicinal plants, especially in the Lamiaceae family.