Genetic variation within and among 12 populations of whip grass in south China were investigated using inter-simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP). High genetic diversity was found in whipgrass by two molecular makers (PPB=86.21%, I=0.357 based on ISSR; PPB=82.21%, I=0.352 based on SRAP). However, there was relatively low genetic diversity at population levels. A high degree of genetic differentiation among populations was detected based on different measures and different molecular markers. We also found that SRAP markers were more efficient than ISSR markers in this species. Based on these findings, sampling strategy was proposed for successfully utilizing the genetic resource of this species.