Developing an understanding of the levels of diversity present at stages across the domestication continuum is key to retaining, or eventually introducing, diversity into domesticated plant lineages. There are special challenges associated with achieving this for perennial crops and their wild relatives, which are often clonal. This is because in species capable of asexual reproduction, it is necessary to first differentiate between clonal ramets and unique genets before measuring genetic diversity. We assessed the clonal structure and genetic diversity in wild populations of lingonberry (Vaccinium vitis-idaea). This survey included 195 individual samples across 15 populations, assayed at 18 nuclear microsatellite loci to reveal the sexual and asexual reproductive strategies of this species. Five of the fifteen populations were found to consist of only two clones each, while other populations maintained a higher number of genetically unique individuals. He across all samples was 0.517 while Ho was higher, at 0.567, with a negative, but nonsignificant, value of FIS (– 0.097 ± 0.038, P = 0.276) across populations. Most of the variation was found within individuals (82%), with a moderate amount of variation between populations (17%), consistent with low levels of population structure at this geographical scale. Wild lingonberry populations at the southern edge of their range in Minnesota exist as both large, clonal organisms and also as mixtures of multiple different clones in a single population. Despite the domination of multiple populations by only a few clones, the species as a whole appears much like a sexually-reproducing species at the genetic level. Some populations are very limited in clonal diversity, meaning that they are subject to extirpation if they fail to thrive under future climatic conditions. This investigation was continued by using eight microsatellite loci to employ clonal analysis and assess the genetic diversity and population structure for 269 V. vitis-idaea samples across modern, historical, world-wide wild, and cultivated groupings. This survey of a perennial, clonal plant over a relatively small geographic range across 50 years did not find clones that persisted over space or time. One location was represented by two preserved herbarium samples, and thorough sampling of that same modern site did not reveal the persistence of a clone after 20 years. The only clones identified from herbarium samples were from the same locations at the same point in time. Performing AMOVA over these four groupings, most of the diversity (72%) was still contained within separate individuals, suggesting weak population structure. As we analyzed population structure across modern, historical, wild, and cultivated groupings, the most surprising result was the differentiation of the modern from the historical grouping. This is indicated by a significant population pairwise FST between the modern and historical grouping (FST = 0.199, P < 0.001), demonstrating an impressive change in lingonberry populations in Minnesota over a contemporary timeframe (from the 1950s to today). Overall, the comparison of historical and modern samples shows that these clonal population dynamics may be variable across time, with high turn-over despite their capacity for asexual reproduction.