Genetic monitoring is a powerful tool to reveal human impact on genetic diversity and genetic differentiation in times of land use and climate change. Unfortunately, it is not yet frequently applied in wild plant nature conservation at present. Consequently, we conducted a genetic monitoring study of the rare and endangered arable weed Sherardia arvensis, which continuously decreased in the recent decades due to environmental changes. Therefore, detecting a possible shift in genetic diversity and differentiation is highly relevant for conservation. We applied multiplexed ISSR genotyping by sequencing (MIG-seq) to compare genetic variation within and among eight populations, as well as effective population size of the species using samples collected at the same sites in 2007 and 2020. We obtained 371 SNPs from 160 analysed individuals. In contrast to our expectations, we observed nearly similar levels of genetic diversity and differentiation within and among populations in 2007 and 2020, although 25% of the investigated populations went extinct in the study period. Effective population sizes showed some differences between the study years, depending on the analysis. The observed maintenance of genetic diversity and differentiation patterns may most likely be explained by the longevity of seeds in the soil, which is generally high in many arable weeds. In the case of S. arvensis seeds may persist in the soil for up to ten years. This allows the regeneration of populations and contributes to the maintenance of genetic variation. A potential impact of population loss and decrease of effective population size on genetic diversity and differentiation may therefore be delayed, comparable to the already described phenomenon of an extinction debt in other species. Our study clearly underlines, that long-term genetic monitoring over long time periods is needed to reveal potential changes of genetic diversity and differentiation in the Anthropocene.