High-quality, chromosome-level genome assemblies of brown algae species, including Scytosiphon promiscuus (male), Dictyota dichotoma (male), Dictyota herbacea (male and female), Ectocarpus crouaniorum (male), Desmarestia dudresnayi (monoicous) and Fucus serratus (male). These assemblies were generated to investigate the structure and evolution of the U and V sex chromosomes in brown algae. Draft genome assemblies were originally obtained from Denoeud et al. (2024) (https://doi.org/10.1016/j.cell.2024.10.049) and subsequently scaffolded to chromosome-level using Hi-C data.