Saccharina japonica, the most extensively farmed seaweed globally, is of great ecological and economic importance. Its applications extend far beyond food consumption, as it is widely utilized in industrial production, biofeed, and medical products, while also playing an important role in marine ecosystems. Its life cycle is characterized by an alternation of generations between haploid gametophytes and diploid sporophytes, with sporophytes typically produced through sexual reproduction. However, S. japonica also exhibits two alternative apomixis reproductive strategies, namely parthenogenesis and apogamy, which bypass fertilization. These asexual modes have attracted increasing attention, as they broaden our understanding of kelp developmental biology and provide new possibilities for germplasm innovation. Epiphytic microorganisms play critical roles in algal growth, morphogenesis, and disease resistance. However, it remains unclear whether sporophytes from different reproductive pathways harbor distinct microbial communities. To address this knowledge gap, we compared bacterial and eukaryotic epiphytic communities of five types of S. japonica sporophytes, representing different reproductive origins and growth states, to reveal differences in community composition, structure, and key biomarker taxa, and explore potential implications for asexual sporophyte development and cultivation. Sporophytes were induced from six female and 15 male gametophyte clones under controlled conditions, including normally growing and malformed parthenogenetic and apogamous sporophytes, as well as normally growing sexually reproduced sporophytes. After 75 days of culture, 39 sporophyte samples were collected. DNA was extracted from surface swabs, and the v3−v4 region of the bacterial 16S rRNA gene and the V4 region of the eukaryotic 18S rRNA gene were sequenced using Illumina NovaSeq 6000 platform. Sequencing reads were quality-filtered, merged, and clustered into operational taxonomic units at 97% similarity based on the SILVA reference database. Alpha diversity was evaluated using Chao1 and Shannon indices, and differences were tested using Student’s t-test. Beta diversity was assessed using non-metric multidimensional scaling (NMDS) based on Bray-Curtis distances and analysis of similarities (ANOSIM). Biomarkers were identified through linear discriminant analysis effect size (LEfSe) using a threshold LDA score ＞4 and P＜0.05. Alpha diversity analysis confirmed that malformed parthenogenetic sporophytes exhibited significantly higher bacterial richness and diversity than all other groups (P＜0.01). Sexual sporophytes showed the lowest alpha diversity in terms of both bacteria and eukaryotes. Apogamous sporophytes, regardless of morphology, generally had a higher diversity than sexual sporophytes, although the differences were not statistically significant. Beta diversity analysis revealed a clear separation of the five groups in the NMDS plots, with ANOSIM confirming significant dissimilarities for both bacterial (R=0.499, P=0.001) and eukaryotic communities (R=0.179, P=0.002). NMDS analysis further indicated that the five sporophyte growth types exhibited significant differences in species composition. In eukaryotic communities, normally growing sexually reproduced sporophytes exhibit the lowest richness and diversity, whereas malformed parthenogenetic sporophytes harbor the most structurally diverse epiphytic assemblages, which may be associated with their distinctive morphological and physiological statuses. Differential taxa among groups were identified using LEfSe and genus-level species composition analyses. Asexual sporophytes generally harbor more enriched bacterial taxa than sexual sporophytes. Malformed parthenogenetic sporophytes contained the highest number of biomarkers, whereas malformed apogamous sporophytes contained the lowest. At the genus level, Litorimonas emerged as the dominant bacterium across multiple groups and was particularly enriched in sexually reproduced sporophytes and malformed apogamous sporophytes. In contrast, the malformed parthenogenetic sporophytes were dominated by unclassified Cyanobacteria, with Litorimonas accounting for a small fraction of the community (3%). The consistent enrichment of Cyanobacteria, which possess an autotrophic capacity and produce antimicrobial metabolites, may partly explain their ecological success. In addition, Maribacter antarcticus was significantly enriched in malformed parthenogenetic sporophytes. Although its precise function remains unclear, its association with abnormal morphology warrants further experimental validation. Eukaryotic communities also exhibited notable variations. Most groups were dominated by Agarum clathratum, a kelp relative species capable of attaching to macroalgae and occasionally acting as a parasite under nutrient-rich conditions. However, malformed parthenogenetic sporophytes were enriched in Halomonhystera, a bacterivorous nematode-like taxon. Its occurrence coincided with higher bacterial loads in these samples, suggesting that host deformities and abundant microbial substrates provided favorable conditions for parasitic colonization. In summary, this study used high-throughput sequencing to systematically analyze the epiphytic microbial diversity of kelp sporophytes derived from sexual reproduction and apomixis. The results revealed significant differences in the microbial community structure between asexual and sexual sporophytes in both the bacterial and eukaryotic communities. Malformed parthenogenetic sporophytes exhibited the most distinct community structure. LEfSe analysis identified significantly different taxa, which enriched the understanding of microbial composition and structure in asexual sporophytes, and offered a solid foundation for future investigations into the interactions between asexual sporophytes and their epiphytic microbiota.