Evaluating the consequences of the decline of threatened species on their population genetic structure is crucial for establishing effective conservation strategies in the strongly fragmented landscapes of Central Europe. Laserpitium prutenicum is a bi- to perennial forb occurring in intermittently wet meadows and light oak forests throughout central to eastern and south-eastern Europe. During the past 70 years, the western limit of its distributional range retracted dramatically, the number of populations decreased and the remaining populations faced a considerable increase of fragmentation. To study the effects of this decline on the genetic diversity of L. prutenicum, we conducted an AFLP study on 20 populations from Germany, Poland and the Czech Republic. For comparison, we collected the same data on Selinum carvifolia, a taxonomically related and both ecologically and morphologically similar species, which is still more common in the study area. Both species showed similarly weak spatial genetic structuring and intermediate genetic diversities. We attribute this result to the loss of habitat being faster than the loss of genetic diversity in smaller and fragmented populations. Depending on the ecological characteristics of a species, even a gradual disappearance is not necessarily accompanied by any detectable effect at the population genetic level (“silent goodbye”). In the case of L. prutenicum, habitat preservation should be given priority over all other conservation measures.