To explore the differential characteristics of epiphytic bacteria in female and male organs of Sargassum fusiforme, this study analyzed community diversity and metabolic function differences of the epiphytic bacteria on the reproductive receptacles and gas vesicles of Sargassum fusiforme by using 16S rRNA high-throughput sequencing technology. The results showed that there were significant differences in the epiphytic bacteria between male and female reproductive organs of Sargassum fusiforme. In terms of community diversity, the α diversity of the epiphytic bacteria on the female reproductive receptacles was higher than that on the male ones. β diversity analysis indicated that gender was the main factor driving the structural differentiation of the epiphytic bacteria on the reproductive receptacles. Regarding community composition, Proteobacteria and Planctomycetota were the dominant bacterial phyla in the reproductive organs of Sargassum fusiforme. The relative abundance of Planctomycetota was higher in the epiphytic bacteria of the female reproductive receptacles and gas vesicles, while Proteobacteria dominated in the epiphytic bacteria of the male reproductive receptacles and gas vesicles. At the genus level, the dominant epiphytic bacterial genera on the female reproductive receptacles were Hellea, Vibrio, and Blastopirellula, while male reproductive receptacles and gas vesicles were primarily dominated by Granulosicoccus and Litorimonas. Metabolic pathway analysis revealed that epiphytic bacteria on female reproductive receptacles exhibited significant upregulation in pathways such as glycosaminoglycan degradation and steroid hormone biosynthesis. In contrast, epiphytic bacteria on male receptacles showed enrichment in carotenoid biosynthesis and oxidative phosphorylation pathways. Compared to male gas vesicles, epiphytic bacteria of the female gas vesicles significantly upregulated pathways including β-lactam resistance, glycosaminoglycan degradation, and sphingolipid metabolism.