We sequenced the epiphytic microbial communities associated with unisexually reproduced sporophytes of Saccharina japonica and compared them with those of sexually reproduced sporophytes to identify differences between the two groups. This work not only expands our knowledge of the composition and structure of the microbiome colonizing unisexual sporophytes, but also lays a solid foundation for future investigations into the interactions between these sporophytes and their epiphytic microbes, as well as for exploring the breeding potential of unisexual sporophytes.