Taxa within the Dactylorhiza incarnata/maculata species complex form a diploid and tetraploid complex. The genetic variation revealed by molecular markers indicate that this is a young complex and that polyploidization may be an ongoing process; most, if not all, of the polyploid taxa may have evolved after the last ice age. This conclusion is supported by 1) a close correspondence in general distribution of nuclear molecular markers in diploids and tetraploids, 2) a close correspondence in marker distribution between diploids and tetraploids occurring in the same geographic area, 3) a low degree of genome reorganization in allotetraploid taxa, and 4) the restricted distribution and endemic nature of several of the allotetraploid taxa in northern areas. A long-term conservation strategy for the complex should concentrate on the parental groups that have contributed to the polyploid genomes. As polyploidization appears to be an ongoing process in the genus, such a strategy would ensure that new polyploids similar to the existing ones may be regenerated if the latter should be lost. Although members of the parental groups are widespread over large parts of Europe, they appear to contain the greatest amount of genetic variation in the south where they have a scattered distribution and may be restricted to specific habitats. However, the polyploids are the important and interesting results of a rapid speciation process. Many of them have restricted distributions in previously glaciated areas in northern Europe, and they are worth protecting on a shorter time scale.