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The diverse offspring of clonal species differ in their dispersability, influencing genotypic diversity and clonal structure. Here, we determined dispersal patterns and their impact on genetic structure in Opuntia microdasys, a self-incompatible cactus with three dispersal units (one sexual and two clonal). We analyzed dispersal, using experiments at three populations, and assessed multilocus genotypes (ISSR markers) of all individuals in 10 clumps per population with known reproductive origin (sexual or clonal). Genotype of all samples, population structure, and migration between clumps and populations were assessed with GenAlEx and GenoDive, assuming higher genotypic diversity and migration when sexual reproduction is more frequent. We determined the most likely number of genetic clusters with STRUCTURE and GENELAND. Dispersal differed among populations; primary dispersal occurred at short distances and was farthest on steep slopes, and dispersal distance increased after secondary dispersal. Clumps had 116 different multilocus genotypes in three spatially explicit genetic clusters. We detected genetic structure at small scale, genotypic diversity among clumps varied between populations; diversity decreased while clonal dominance increased, and the most variation occurred among clumps. Genetic structure was moderate, suggesting gene flow by seed dispersal allows slight differentiation among population at large scales. Genetic diversity within clumps was the lowest because dispersal of clonal propagules was limited and caused genotypic dominance at local scale. However, the combined dispersal pattern of sexual and clonal dispersal units is fine-tuned by environmental factors, generating a range of genetic diversity among clusters and populations. This pattern suggests that genetic structure of clonal plants is more dynamic than thought, and dispersal of different types of offspring affects genetic structure at many scales.