PKS gene was screened by PCR from thirty strains of spone-associated bacteria including twenty-one actinomycetes isolated from Craniella anstrialiensis and nine bacillus isolated from Dysidea avara in the South China Sea. As a result, a 669 bp KS domain gene was successfully amplified from Bacillus C89. BLAST analysis showed that the KS domains were most closely related to the KS sequences of Bacillus subtilis subsp.subtilis str.168 with 96% similarity. Phylogenetic analysis demonstrated the KS domain belong to trans-AT KS domains. This study demonstrated the existence of PKS gene in bacteria associated with sponge Dysidea avara for the first time, and provided proof for the hypothesis that sponge-associated bacteria are perhaps the true producers of many novel bioactive compounds in sponge. Meanwhile, this study lays a basis for the microbial screening for polyketide compounds production.