The fine-scale clonal structure in the patch of the invasive plant Mikania micrantha H.B.K. and its plant parasite Cuscuta campestris Yunker were investigated by distinguishing genets using ISSR markers. A high level of clonal diversity (G/N = 0.7, D = 0.9579, E = 0.7778) in M. micrantha and a low level of clonal diversity (G/N = 0.2, D = 0.7632, E = 0.9479) in C. campestris might be due to the different reproductive strategies, different migration rates and different number of founder. Clonal composition of M. micrantha (14 genets of 20 ramets) and C. campestris (4 genets of 20 ramets) were significantly different. There was no relationship between host and parasite genetic distance matrices using Mantel test (r = 0.073, P = 0.150). Spatial autocorrelation analysis of M. micrantha showed that the correlation value was positive and significant at 2 m with an x-intercept of 3.5 and 4.0 m for distance class sizes of 1 and 2 m, respectively. Spatial autocorrelation analysis of C. campestris showed that the correlation value was positive and significant at 2 m and significantly negative at 10 m with an x-intercept of 4.8 and 6.6 m for distance class sizes of 1 and 2 m, respectively.