Nonribosomal peptide synthetase (NRPS) adenylation (A) domain genes were investigated by polymerase chain reaction for 109 bacteria isolated from four South China Sea sponges, Stelletta tenuis, Halichondria rugosa, Dysidea avara, and Craniella australiensis. Meanwhile, the antimicrobial bioassay of bacteria with NRPS genes were carried out to confirm the screening of NRPS genes. Fifteen bacteria were found to contain NRPS genes and grouped into two phyla Firmicutes (13 of 15) and Proteobacteria (two of 15) according to 16S rDNA sequences. Based on the phylogenetic analysis of the conserved A domain amino acid sequences, most of the NRPS fragments (11 of 15) showed below 70% similarity to their closest relatives suggesting the novelty of these NRPS genes. All of the 15 bacteria with NRPS genes have antimicrobial activities, with most of them exhibiting activity against multiple indicators including fungi and gram-positive and gram-negative bacteria. The different antimicrobial spectra indicate the chemical diversity of biologically active metabolites of sponge-associated bacteria and the possible role of bacterial symbionts in the host's antimicrobial chemical defense. Phylogenetic analysis based on the representative NRPS genes shows high diversity of marine NRPS genes. The combined molecular technique and bioassay strategy will be useful to obtain sponge-associated bacteria with the potential to synthesize bioactive compounds.