Abstract:With the combination of ISSR (inter-simple sequence repeats), SRAP (sequence-r elated amplified polymorphism) and spatial autocorrelation, the genetic diversit y and spatial structure per unit patch of three Huaiyuan populations of Thymus quinquecostatus in southeast China were analyzed. The results showed that there e xisted higher levels of genetic and clonal diversity among the patches within th e wild T. quinquecostatus populations, with the percentage of polymorphic lo c being 7575%, Nei’s gene diversity being 02537, Shannon’s information ind ex being 03811, percent of genetype (G/N) being 061, Simpson index (D) bein g 096, and Fager index (E) being 091. Analysis of molecular variance (AMOVA) showed that only 965% of genetic variation resided among the populations, whi le 9035% of it resided among the individuals within the populations. No genoty pe patches in common were observed among the three populations. The spatial dist ribution of the same patches showed a concentrated distribution about 0〖KG-*2〗 -〖KG-*7〗25 m, and that of different patches showed an inlaid distribution. Exc ept for some locations that showed par correlations in the Huaiyuan populations of T. quinquecostatus, most locations lacked in spatial structure according to spatial autocorrelation analysis. The possible mechanism causing the establis hment of the patches of T. quinquecostatus populations was due to seed dispe rsing, and the following clonal reproduction played important roles in patch dev elopment and population expanding.