In order to identify the strain of Streptococcus iniae(S.iniae) from the infected tilapia at molecule level, the 16S rRNA gene was amplified by using the universal primers, and the PCR product was cloned and sequenced．A sequence of 1447 base pair(bp) was obtained from the bacteria．The sequence was compared to that derived from GenBank using BLASTn，and the closest sequence was the 16S rRNA gene of S.iniae SCCF5L strain，with a similarity of 99.4% and we name it S.iniaeCGX strain. The phylogenetic analysis was based on the 16S rRNA genes sequences of S.iniaeCGX strain and other related organisms，including the representative strains of S.iniae, S.difficilis and S.agalactiae species in GenBank database. The result showed that all strains of S.iniae specie formed a separate and distinct phylogenetic branch, the strains of S.difficilis and S.agalactiae species formed another two separate and distinct phylogenetic branches. The results above showed that the strain of Streptococcus from the tilapia brain was S.iniae species.