Typha minima was formerly widespread along fast flowing alpine rivers but is now red-listed as critically endangered. To assess its conservation perspectives, we surveyed the few remaining natural populations along the alpine part of the River Rhine from 1997 to 2002 and determined their genetic diversity using isozyme electrophoresis. Six of the populations became extinct or extremely small, probably due to shading by taller plants and trampling, while six other populations remained stable or increased, partly due to habitat restoration measures. The largest populations, with areas of more than 10’000 m², are found in secondary habitats which are regularly disturbed due to water regime management. Of the 19 investigated isozyme loci, only six were polymorphic. Allelic diversity (1.4–1.8) was low in all populations, and the number of multilocus genotpyes (1–18) was low for 11 of 13 investigated populations. Genetic diversity was also studied for ex-situ cultivations of T. minima in Swiss botanical gardens and reintroduced stands. These artificial populations (each with 1–3 multilocus genotypes) were genetically similar to natural populations (average genetic distance 0.094). For two ex-situ cultivations with unknown origin, the likely origin could genetically be defined. Hybridisation between two ex-situ cultivations of different origin (i.e. a potential risk of genetic introgression) was detected in one botanical garden. It is concluded that the long-term conservation of T. minima requires both the restoration of regularly disturbed, sparsely vegetated river margins and the re-introduction of plants from ex-situ cultivations with appropriate origin.