Sugarcane white leaf (SCWL), associated with the presence of “CandidatusPhytoplasma sacchari,” is a devastating disease. In this study, a multilocus sequence typing (MLST) scheme based on seven housekeeping genes (dnaK, tuf, secY, gyrB, secA, recA, and hflB) was applied to examine the genetic diversity and population structure of “Ca.P. sacchari.” Using this MLST scheme, 87 “Ca.P. sacchari” infected sugarcane samples from Yunnan province, China, were analyzed, and two sequence types (STs) were identified. ST1 is the most widely distributed and is the main ST, whereas ST2 is only found in the Baoshan area in China. Analysis of the population structure showed that the ST1 and ST2 “Ca.P. sacchari” were the different populations. The nucleotide diversity of the seven housekeeping genes ranged from 0 to 0.00268, indicating that the genetic diversity of “Ca.P. sacchari” in China is very low. The MLST scheme developed offers researchers a valuable typing tool for epidemiology and diversity studies of “Ca.P. sacchari.”