Over the last decade there has been a tremendous increase in the use of flow cytometry (FCM) in studies on the biosystematics, ecology and population biology of vascular plants. Most studies, however, address questions related to differences in genome copy number, while the value of FCM for studying homoploid plant groups has long been underestimated. This review summarizes recent advances in taxonomic and ecological research on homoploid plants that were made using FCM. A fairly constant amount of nuclear DNA within each evolutionary entity together with the often large differences between species means that genome size is a useful character for taxonomic decision-making. Regardless of the number of chromosomes, genome size can be used to delimit taxa at various taxonomic levels, resolve complex low-level taxonomies, assess the frequency of interspecific hybridization or infer evolutionary relationships in homoploid plant groups. In plant ecology and evolutionary biology, variation in genome size has been used for prediction purposes because genome size is associated with several phenotypic, physiological and/or ecological characteristics. It is likely that in the future the use ofFCM in studies on taxonomy, ecology and population biology of homoploid plants will increase both in scope and frequency. Flow cytometry alone, but especially in combination with other molecular and phenotypic approaches, promises advances in our understanding of the functional significance of variation in genome size in homoploid plants.