In 2009, a Brucella suis biovar 3 case was first reported in Hainan province. To compare the epidemiological relationship between strains of B. suis biovar 3 recently isolated from China and exogenous strains, a multiple-locus variable-number tandem-repeat analysis (MLVA) was used. The 26 strains clustered together with B. suis biovar 3 reference strain REF686, sharing all panel 1 (genotype 4: 2-3-4-11-3-1-5-2) and panel 2A (genotype 15: 4-19-9) markers. The most discriminatory VNTR markers were bruce09, with a diversity index of 0.85, consisting of eight alleles. However, we have not found the host specific genotypes (human versus animal). MLVA genotyping analysis should enable the improvement of brucellosis surveillance and control programs focused on safeguarding public health.