To explore the bacterial community structure on the surface of healthy and diseased seedlings of Saccharina japonica during a temporary rearing period and their relationships with seawater, in this study, sequences of 16S rRNA from healthy kelp (HS), diseased kelp (DS), seawater from healthy kelp breeding areas (HW), and seawater from diseased kelp breeding areas (DW) were analyzed using Illumina sequencing technology. The results showed that 32 phyla, 77 classes, 398 families, 797 genera, and 1772 operational taxonomic units (OTUs) were identified. At the phylum level, the dominant bacteria in the kelp samples were Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes. The relative abundances of Bacteroides, Actinobacteria, and Firmicutes in the HS and DS samples were 19.91%, 10.79%, 15.52%, 37.31%, 1.65%, and 5.92%, respectively, showing substantial differences. At the family level, the relative abundances of Flavobacteriaceae and Rhodobacteraceae in the HS samples were 10.7% and 12.55%, respectively, which was lower than those in the DS samples (33.47% and 21.17%, respectively). The diversity analysis showed that the Ace and Chao indexes between HS and DS samples showed no significant differences (P>0.05), whereas the Shannon and Simpson indexes showed significant differences (P<0.05). The SIMPER analysis showed that the four OTUs (OTU1169, OTU1111, OTU1351, and OTU1353) from the three bacterial families in the diseased kelp provided a difference rate of 35.88%. In summary, the relative abundances of dominant epiphytes in healthy and diseased kelp were significantly different, as was the distribution between species (P<0.05), but there was no significant difference in species richness. OTU1169 and OTU1111, belonging to the flavobacteria, were the main indicators for the diagnosis of diseases in kelp. This study analyzed the interaction between epiphytes and vegetative kelp diseases from the perspective of community structure and diversity and provided a scientific reference for revealing the mechanism of vegetative kelp diseases in the future.