Sporeling malformation disease, characterized by abnormal cell proliferation and tissue disintegration, causes catastrophic losses in the seedling production of kelp Saccharina japonica. Previous efforts have implicated diverse factors responsible for disease occurrence, including environmental stressors (eg, inadequate light exposure), maturity of parental kelp (eg, unmatured or overmatured), alginate-decomposing bacteria, and so on. Traditional culture-dependent approaches, focusing on sulfate-reducing bacteria and alginate-decomposing bacteria, determined potential relationships with disease occurrence, indicating the role played by the epiphytic bacterial members. However, these studies failed to explain the complex pathogenesis, and the precise microbial etiology remains elusive. Recent advances in holobiont theory suggest that the dysbiosis of epiphytic microbiota, rather than individual pathogens, could drive disease progression. Our previous study has also shown that dysbiosis of the epiphytic bacterial community correlates with the severity of sporeling malformation disease, and this disruption, in turn, might modify host–bacteria interactions to enhance disease severity. In the present study, by analyzing the diversity, structure, and functional profiles of the epiphytic bacteria on sporelings with different malformation rates, we seek to obtain more data related to the relationships between the epiphytic bacterial communities and the incidence of sporeling malformation disease using in situ sporeling samples. Through microscopic observation in 2018, two groups of biological samples (i.e., the Low and High groups) were collected from a workshop in a typical kelp seedling hatchery in Weihai, China. The malformation rate in the Low group was estimated to be approximately 2~6%, while that in the High group reached approximately 10~12%. Epiphytic bacterial DNA was extracted from the samples and the hypervariable regions V5-V7 of the 16S rRNA gene were amplified and sequenced using the Illumina NovaSeq platform. The sequences were processed using USEARCH and QIIME for quality control, chimera removal, denoise, and taxonomic assignment. Alpha and Beta diversity analyses were performed to compare the bacterial community diversity and structure between the two groups. LEfSe analysis was used to identify differentially abundant bacterial taxa, and PICRUSt2 was employed to predict the functional profiles of the epiphytic bacterial communities. The results showed that the Alpha diversity indices of the bacterial communities in the High group were significantly lower than those in the Low group, except for the Shannon index, indicating a reduced richness of bacterial communities in the High group. Principal coordinates analysis (PCoA) based on Bray-Curtis distances revealed a distinct separation of the bacterial community structures between the Low and High groups with 32.74% variance explained by PCo1, although not significant (Adonis R2=0.28, P=0.10). Whereas, inter- and intra-group comparisons of Bray-Curtis distances did reveal significant differences (one-way analysis of variance [ANOVA] with Tukey’s test, P = 0.029 < 0.05), indicating significant community structure associated with sporelings with different malformation rates. The bacterial phyla in both groups were dominated by Alphaproteobacteria (51.9%±0.1%), Gammaproteobacteria (19.8%±1.3%), Deltaproteobacteria (14.4%±3.3%), and Bacteroidetes (9.7%±1.2%), and the predominated bacterial genera included Halobacteriovorax, Thalassospira, Methylotenera, Nautella, and Marinobacter. Their relative abundances were different between the Low and High groups, which further indicated the community transition from low to high disease severity. By exploring differentially abundant taxa, it is determined that the Low group tended to be enriched in mutualists, such as Hyphomonas and Amorphus (morphogenesis inducer), Flexivirga and Curtobacterium (plant growth promoter), and bacterial members in Bacteroidetes (common colonizer and morphogenesis inducer). In comparison, putative pathogenic taxa were determined to be more abundant in the High group. For example, Pelagibacterium (FicT toxin carrier to kill the host), Acidovorax (phenolic compound degrader to facilitate invasion), and Rhodococcus (toxin carrier and phytohormone disruptor). From a functional perspective, the Low group had a higher abundance of pathways related to growth, development, and defense, such as pyrimidine metabolism, vitamin and coenzyme A synthesis, and immune defense. In comparison, functional prediction analysis indicated that the High group upregulated xenobiotic degradation (benzoate and steroids), limonene and pinene degradation, and virulence-associated polysaccharide biosynthesis (arabinoglyctan and lipoarabinomannan biosynthesis). The present study provides new insights into the microbial mechanisms underlying sporeling malformation disease. The significant differences in the structure and function of the epiphytic bacterial communities between the Low and High groups suggest that the disruption of the bacterial community may contribute to the development of the disease, which is consistent with our previous study. The 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 the changes in whole community functions using different omics methods and exploring 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. By identifying key microbial taxa and functional pathways associated with the disease, the findings may guide the development of microbial-based strategies for disease management, thereby contributing to the sustainable development of kelp cultivation.