Isolated populations are likely to experience a loss of genetic diversity because of reduced gene flow, and the effects of habitat fragmentation are, therefore, central issues in conservation genetics. Here, we present data on genetic diversity and isolation-by-distance for the rare central Asian plant Potentilla ikonnikovii (Rosaceae), which occurs in naturally fragmented populations. Sampling covered the entire distributional range of this endemic of southern Mongolia, where the species is restricted to archipelago-like mountain systems that emerge from the semidesert lowlands of the Gobi region. Random amplified polymorphic DNA analyses revealed modest levels of genetic diversity at both the population and species level. A Φ_ST of 0.68 indicates that isolation has strong effects on population genetic structure; most variance is kept among populations rather than within, and the two most remote populations were genetically distinct. Mantel statistics showed that genetic distance was highly correlated to spatial distance (R_M > 0.6). We conclude that populations of P. ikonnikovii are severely isolated in terms of genetic structure. This may lead to reduced fitness and a crude monitoring scheme is recommended.