Aims Isolating culturable bacteria associated with sea cucumber (Apostichopus japonicus) and investigating their potential bioactivities are important approaches to discover natural marine products. Methods and Results A total of 161 isolates were obtained from sea cucumber collected along the Weihai coast of the North Yellow Sea, China. Identification and phylogenetic analysis of 61 isolates were conducted by 16S rRNA gene sequencing. The isolates belonged to 13 genera from 10 families in three phyla, including Firmicutes, Actinobacteria and Proteobacteria. The antimicrobial activities of all strains were determined using six indicator strains. Of the 161 isolates, 93 showed antibacterial activities against at least one of the indicator strains. The 26 strains with the strongest inhibitory effects were selected for screening the biosynthetic gene clusters of polyketide synthase (PKS-I, -II) and nonribosomal peptide synthetase (NRPS). Phylogenetic trees based on the amino acid sequences of the PKS or NRPS genes were constructed. Eleven strains with PKS genes and four strains with NRPS genes were detected. Conclusions The data reveal the diversity of culturable bacteria associated with A. japonicus. Most strains showed broad-spectrum antimicrobial activities, and some strains with antimicrobial activities possessed PKS and NRPS genes. Significance and Impact of the Study The results suggest that culturable bacteria associated with A. japonicus may act as a promising source of bioactive substances.