Genetic diversity, clonal diversity and clonal structure within the patches of the stoloniferous herb Duchesnea indica Focke were analyzed using inter\|simple sequence repeat (ISSR) techniques. The relationship between clonal structure and habitat conditions was also studied to elucidate how clonal structure of D. indica was established. Genetic diversity of D. indica was relatively low: percentage of polymorphic loci (P) 37.93%, Shannon informative index (I) 02402, and Nei′s gene index (h) 0.1677. Clonal diversity of D. indica was similar to that of other clonal plant species. The proportion of distinguishable genotypes (G/N) was 0.2013, Simpson′s diversity index (D) 0.6396 and genotypic evenness (E) 0.5862. Both genetic diversity and clonal diversity of D. indica were the highest within the patch in Linhai City (LH), lowest within the patch in Tiantai City (TT), and intermediate within the patch in Anju City (AJ). Dominant clones were found in all three patches, but their size was the largest in the TT path, smallest in the LH patch and intermediate in the AJ patch. Spatial autocorrelation analysis showed that in the LH patch the autocorrelation coefficient was significantly positive at distances of 20 cm and 40 cm with an X\|intercept of 49.959. In the AJ patch the correlation value was significantly positive at 20 cm with an x\|intercept of 63.333 and in the TT patch it is positive and significant at 20 cm, 30 cm, 40 cm and 70 cm, respectively, with an X\|intercept of 90.512. This indicates that the spatial autocorrelation scale of the genotype was highest within the TT patch, lowest in the AJ patch, and that the average length of genetic patches was the largest in the TT patch and smallest in the LH patch. The genetic diversity, clonal diversity and clonal structure of D. indica in three different patches were significantly different, which might be due to vegetative spreading and also the low seed germination rate. The ecological factors, together with others such as disturbance, succession and mutation, might have played important roles in the formation of the genetic structure, clonal structure and spatial distribution patterns.