The pathogenic bacteria of seaweed diseases are mostly the opportunistic pathogenic bacteria. In this study, an opportunistic pathogenic bacterium MS-3 was isolated and identified from healthy mature sporophytes of Saccharina japonica by combining the traditional culture-dependent method, bacteria-S. japonica infection assay and 16s rRNA gene sequence comparison. Through the infection assay and microscopic observations, it was shown that strain MS-3 can cause green-rotten diseased symptom in S. japonica after infected at 6 h under laboratory condition. The colony of MS-3 was round and bright yellow. The cells of MS-3 were rod shaped with a single polar flagellum. MS-3 had the highest similarity of 99.7% with Vibrio neocaledonicus NC470 by comparing 16s rRNA gene sequences. Combining the physiological and biochemical characteristics of MS-3, we identified it as Vibrio neocaledonicus MS-3. Our results not only enrich the strain resource of opportunistic pathogenic bacteria of S. japonica and lay a foundation for investigating the pathogenic mechanisms of the opportunistic pathogenic bacteria, but also help to develop the diagnostic technology for S. japonica diseases.