Charophyceae, relatives of land plants, have genomes that present important information to understand how land plants evolved from their ancestors in the Paleozoic era. Here, we report the draft genome of Chara braunii from Charophyceae, and its comparison to land plants, Klebsormidium nitens, and other green algae. The comparison revealed acquisition of genes before and after the divergence of Charophyceae in the lineage leading to land plants, as well within Charophyceae.