Accumulative evidence has supported the pivotal roles of gut microbiota in shaping host health in a wide range of animals. However, the relationship between gut microbiota and sea cucumber disease is poorly understood. Using the Illumina sequencing of bacterial 16 S rRNA gene, we investigated the divergence of gut bacterial communities between healthy and skin ulceration syndrome (SUS) diseased Apostichopus japonicus. The results showed that bacterial phylotypes in both groups were closely related at phylum level with predominant component of Proteobacteria (>90%). However, Firmicutes and Verrucomicrobia displayed opposite trends in two groups with higher abundance of Firmicutes and lower of Verrucomicrobia in diseased group. Further KEGG enrichment revealed that bacterial-mediated infectious diseases and signal transduction pathways were significantly induced in the SUS group. We also identified one OTU of Lactococcus garvieae from Firmicutes exhibited significantly different abundances in diseased sea cucumber as compared to healthy subjects. The relative abundance of the species was 27.67% ± 10.52% in diseased group compared to 2.78% ± 2.59% in healthy sea cucumber. Three virulence genes of hlyIII, fbp and pva encoded by L. garvieae were investigated by qPCR, and were found to be significantly induced (P < 0.05) in diseased sea cucumbers as compared to healthy ones. All our results supported that L. garvieae might be a potential pathogen for SUS outbreak and could be served as a bio-indicator for this disease monitoring.