The Carex flava complex ( Cyperaceae) was used as a model system in a study of the effects of variation in species delimitation on genetic diversity estimates. The whole complex constitutes a syngameon within which gene flow may occur between taxa. Several more or less distinct evolutionary lineages in the complex are morphologically similar to each other and are often combined into broadly defined taxonomic species. Separate calculations of genetic diversity estimates for the most narrowly defined species revealed clear differences between some of the taxa; for instance, C. flava s. s. had a very low value for individual gene diversity, H-1 whereas C. hostiana and C. lepidocarpa ssp. lepidocarpa had high values for total genetic diversity, H-T Amounts of genetic diversity at different hierarchic levels ( H-T, H-S, H-I) generally increased as narrowly defined species were combined into more broadly defined species. However, combining ecological species ( ecotypes) within C. oederi s. l. had little effect on estimates of genetic diversity. The proportion of genetic diversity due to variation between populations, G(ST), increased initially as ecologically and/ or geographically separated lineages were amalgamated, but decreased as the species were even more boradly circumscribed to include distinct lineages growing in mixed populations. The proportion of genetic diversity due to variation between individuals within populations ( numerically equivalent to the inbreeding coefficient, F-IS) was dependent on the degree of hybridization and introgression at sites with mixed populations and was found to increase or decrease when taxa became more broadly circumscribed. It is concluded that differences in species circumscription may have dramatic effects on genetic diversity estimates, and it is recommended that calculations should be performed separately for separate evolutionary lineages in order to obtain comparable estimates for different plant groups.