Abstract
Habitat fragmentation is known to cause genetic differentiation between small populations of rare species and decrease genetic variation within such populations. However, common species with recently fragmented populations have rarely been studied in this context. We investigated genetic variation and its relationship to population size and geographical isolation of populations of the common plant species, Lychnis flos‐cuculi L., in fragmented fen grasslands. We analysed 467 plants from 28 L. flos‐cuculi populations of different sizes (60 000–54 000 flowering individuals) in northeastern Switzerland using seven polymorphic microsatellite loci. Genetic differentiation between populations is small ( F ST = 0.022; amova ; P H O = 0.44) significantly deviates from Hardy–Weinberg equilibrium, and within‐population inbreeding coefficient F IS is high (0.30–0.59), indicating a mixed mating breeding system with substantial inbreeding in L. flos‐cuculi . Gene diversity is the only measure of genetic variation which decreased with decreasing population size ( R = 0.42; P L. flos‐cuculi , the lower gene diversity of smaller populations suggests that the species is not entirely unaffected.