Patterns of ploidy variation can provide useful insights into the evolutionary mechanisms that shape the dynamics of plant systems showing ploidy diversity. Trávníček et al. examine cytotype variation in fragrant orchids, Gymnadenia species, at different spatial scales, from transcontinental to intra-populational. They find that most Gymnadenia populations exhibit considerable cytogenetic (and, to a lesser degree, taxonomic) heterogeneity. In contrast to previously investigated plant groups, Gymnadenia is unique in that it is the incidence of rare minority cytotypes that largely drives intra-population ploidy variation. The cytogenetic structure of Gymnadenia populations is remarkably dynamic and shaped by multiple evolutionary mechanisms, including both the ongoing production of unreduced gametes and heteroploid hybridization.