Tetraploid Ficaria verna is a common spring geophyte that forms large populations in central Europe and is considered invasive in northern USA and Canada. It is considered an almost seed-sterile taxon, relying on vegetative reproduction by underground tubers and aerial bulbils. Recent studies have revealed high levels of population genetic diversity in F. verna, raising the question of how genetic diversity is maintained and which factors may be responsible for the observed patterns. Polymorphic nuclear microsatellite markers were established to define multi-locus genotypes (MLGs), to analyze fine-scale spatial genetic structure (SGS) using grid and cross sampling schemes, and to quantify genetic diversity within and between nine populations with different disturbance regimes in central Germany. 115 MLGs were identified among a total of 347 samples. The G/N ratio varied between 0.16 and 0.70 among populations, and in each population a number of unique MLGs occurred. Genotypes were highly intermingled within populations, suggesting a ‘guerrilla’ dispersal strategy. Significant negative SGS was found in five out of nine populations in fine-scale cross sampling (up to 4 m) and in only one population in grid sampling (up to 14.6 m). No single MLG was found in more than one population, while many alleles were shared between populations. Within-population genetic diversity increased with greater exposure to both anthropogenic and natural disturbances. Regular gap openings, facilitated propagule establishment (vegetative and sexual), and propagule dispersal by water and mowing machines are likely important factors explaining the positive effects of disturbance on local genetic diversity of F. verna.