Sporeling malformation disease, characterized by abnormal cell proliferation and tissue disintegration, causes catastrophic losses in the seedling production of kelp Saccharina japonica. Previous studies have linked disease occurrence to environmental stressors (e.g., inadequate light exposure), the maturity of parental kelp (e.g., immature or overmatured), and alginate-decomposing bacteria, among others. Traditional culture-dependent approaches have failed to explain the complex pathogenesis of this disease, and its precise microbial etiology remains elusive. Recent advances in holobiont theory and our previous work suggest that dysbiosis of epiphytic microbiota, rather than individual pathogens, may drive sporeling malformation by disrupting host-microbe interactions and exacerbating disease severity. In the present study, we analyzed the diversity, structure, and functional profiles of epiphytic bacteria on sporelings with different malformation rates to obtain more data related to the relationships between epiphytic bacterial communities and the incidence of sporeling malformations using in situ sporeling samples. Through microscopic observations, in 2018, two groups of biological samples (Low and High groups) were collected from a workshop in a typical kelp seedling hatchery in Weihai, China. Epiphytic bacterial communities from low (~2%–6%) and high (~10%–12%) malformation groups were analyzed using 16S rRNA sequencing. Bioinformatic analyses (QIIME, USEARCH, LEfSe, and PICRUSt2) were used to assess community diversity, identify differential taxa, and predict functional profiles. Alpha diversity was lower in the high-malformation group. This indicated reduced bacterial richness. Community structure differed significantly between groups, with distinct shifts in dominant taxa. The low group demonstrated a higher presence of mutualistic and morphogenesis-associated bacteria. Meanwhile, the high group displayed more taxa associated with pathogenicity. The low group was more closely linked to metabolic and defense-related pathways. In contrast, the high group was associated with xenobiotic degradation and virulence-related functions. These findings highlight the importance of maintaining a healthy microbial community for sporeling growth and development and suggest potential targets for disease prevention and control. Future research should focus on changes in whole community functions using different omics methods and explore the interactions between the host, environment, and certain isolated bacterial strains in the context of disease development. This study not only enriches our understanding of the microbial ecology of kelp diseases but also has important practical implications for the kelp farming industry. Identifying key microbial taxa and functional pathways associated with disease may guide the development of microbial-based strategies for disease management, thereby contributing to the sustainable development of kelp cultivation.