Abstract: Objective To investigate the variations of the capsular polysaccharide synthesis gene (cps)cluster sequences of 41 non-serotypeable Streptococcus suis (S. suis). Methods The cps sequences were extracted from draft sequences which were released from GenBank database according to the accession numbers. The cps types of non-serotypeable strains were defined based on their wzy sequences and cps loci were compared with corresponding reference strains and analyzed. Results The cps types of 37 non-serotypeable strains were assigned to known reference serotypes. Insertion, deletion, inversion, replacement and frameshift mutation of some cps genes were found in 18 of the 37 strains. The cps sequences of 16 non-serotypeable strains shared high similarity with those of reference strains (over 99%), meanwhile the identity of cps cluster sequences from strain LSS23, LSS31, LSS37 to their reference strain 88-5299A (serotype 24) was 96%. Four non-serotypeable strains carrying known novel cps loci were also found. Conclusion The sequence variation of cps loci of S.suis is ongoing, which cannot be identified effectively by serum agglutination. A more sensitive molecular serotyping strategy is needed.