Wolbachia is a maternally inherited bacterium of insects that can alter the reproduction, biology, and fitness of the hosts. It was detected in natural populations of the Yamatotettix flavovittatus Matsumura leafhoppers, the vector of phytoplasma, which is responsible for sugarcane white leaf disease. Wolbachia infection prolongs the longevity of female leafhoppers and promotes a strong reproductive incompatibility; importantly, highly maternal transmission rate was observed. However, limited data on the diversity or strain typing of Wolbachia in Y. flavovittatus are available. We aimed here to detect the presence of Wolbachia in different populations by amplification of the wsp gene, which was then sequenced. Multilocus sequence typing (MLST) was also performed to explore the diversity of the Wolbachia strains. Based on the wsp sequences, Wolbachia in the Y. flavovittatus leafhoppers belonged to supergroup B, and formed a distinct evolutionary lineage; therefore, we designated this new specific strain as wYfla. The MLST profiles revealed ten potential new sequence types (STs) in different leafhopper populations. Multiple STs were detected in individual leafhoppers, among which the ST-wYfla1 strain was predominant. Furthermore, we obtained congruent results for the phylogenetic analyses using the wsp gene and MLST loci. To the best of our knowledge, this is the first study characterizing Wolbachia strains in Y. flavovittatus. Our results reveal a novel strain and multiple STs of Wolbachia, and these data may prove useful in the exploitation of Wolbachia as a biological Y. flavovittatus control agent.