Mycoplasma synoviae (M. synoviae) infection leads to serious economic losses in the world every year. Between 2013 and 2014, the infectious synovitis, caused by M. synoviae infection, occurred in native chickens in China and resulted in the loss of millions of chickens in Chinese poultry farms. However, there has been no data about phylogenetic and pathogenic analysis of Chinese M. synoviae isolates. In this study, a total of 110 M. synoviae strains were isolated from M. synoviae infected chickens. The isolates identified in the present study were classified into a new distinct subgroup based on analysis of the 5′-end vlhA sequences, tentatively termed the K group. In addition, though the pathogenicity was significantly different among isolates, there was no close relationship between pathogenicity and genotype for Chinese M. synoviae based on a pathogenic analysis of the 5′-end of the vlhA gene.