Tussocks are unique vegetation structures in wetlands. Many tussock species mainly reproduce by clonal growth, resulting in genetically identical offspring distributed in various spatial patterns. These fine-scale patterns could influence mating patterns and thus the long-term evolution of wetland plants. Here, we contribute the first genetic and clonal structures of two key species in alpine wetlands on the Qinghai-Tibet Plateau, Kobresia tibetica and Blysmus sinocompressus, using > 5000 SNPs identified by 2b-RAD sequencing. The tussock-building species, K. tibetica, has a phalanx (clumping) growth form, but different genets could co-occur within the tussocks, indicating that it is not proper to treat a tussock as one genetic individual. Phalanx growth does not necessarily lead to increased inbreeding in K. tibetica. B. sinocompressus has a guerilla (spreading) growth form, with the largest detected clone size being 18.32 m, but genets at the local scale tend to be inbred offspring. Our results highlight that the combination of clone expansion and seedling recruitment facilitates the contemporary advantage of B. sinocompressus, but its evolutionary potential is limited by the input genetic load of the original genets. The tussocks of K. tibetica are more diverse and a valuable genetic legacy of former well-developed wet meadows, and they are worthy of conservation attention.