Saccharina japonica, the most extensively farmed seaweed in the world, is a kelp 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, not only because they broaden our understanding of kelp developmental biology, but also because they 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, the present study systematically compared bacterial and eukaryotic epiphytic communities on five types of S. japonica sporophytes, representing different reproductive origins and growth states, aiming to reveal differences in community composition, structure, and key biomarker taxa, and to explore potential implications for asexual sporophyte development and cultivation. Sporophytes were induced from six female and fifteen 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, a total of 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 the Illumina NovaSeq 6000 platform. Sequencing reads were quality-filtered, merged, and clustered into operational taxonomic units (OTUs) at 97% similarity, with taxonomic assignment based on the SILVA reference database. Alpha diversity was evaluated using Chao1 and Shannon indices, with differences tested by Student’s t-tests. 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 of 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 for both bacteria and eukaryotes. Apogamous sporophytes, regardless of morphology, generally had higher diversity than sexual sporophytes, though the differences were not statistically significant. Beta diversity analysis revealed clear separation of the five groups in 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 growth types of sporophytes exhibited significant differences in species composition. For eukaryotic communities, normally growing sexually reproduced sporophytes exhibited the lowest richness and diversity, whereas malformed parthenogenetic sporophytes harbored the most structurally diverse epiphytic assemblages, which may be associated with their distinctive morphological and physiological status. The differential taxa among groups were identified using LEfSe and genus level species composition analysis. Asexual sporophytes generally harbored more enriched bacterial taxa than sexual sporophytes. Malformed parthenogenetic sporophytes contained the highest number of biomarkers, while malformed apogamous sporophytes contained the fewest. At the genus level, Litorimonas emerged as a dominant bacterium across multiple groups and was particularly enriched in sexually reproduced sporophytes and malformed apogamous sporophytes. By contrast, malformed parthenogenetic sporophytes were dominated by unclassified Cyanobacteria, with Litorimonas accounting for only a small fraction of the community (3%). The consistent enrichment of Cyanobacteria, which possess autotrophic capacity and produce antimicrobial metabolites, may partly explain their ecological success in this context. In addition, Maribacter antarcticus was found to be significantly enriched in malformed parthenogenetic sporophytes. Although its precise function remains unresolved, its association with abnormal morphology warrants further experimental validation. Eukaryotic communities also exhibited notable variation. The majority of 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 with Halomonhystera, a bacterivorous nematode like taxon. Its occurrence coincided with the 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 microbial community structure between asexual and sexual sporophytes for both bacterial and eukaryotic communities. Notably, malformed parthenogenetic sporophytes exhibited the most distinct community structures. LEfSe analysis identified significantly different taxa, which not only enriched the understanding of microbial composition and structure in asexual sporophytes but also provided a solid foundation for future investigations into the interactions between asexual sporophytes and their epiphytic microbiota.