Genetic structure and diversity were studied in the endangered peatmoss Sphagnum angermanicum Melin to assess its conservation status. In total, 128 shoots from eleven populations throughout its Swedish distribution were analyzed. Among these shoots 28 haplotypes were identified by 19 ISSR loci. The most common haplotype (50% of the sampled shoots) occurred in all populations. The level of gene diversity over loci was intermediate compared to records from most other bryophytes. There was no genetic isolation between the populations and most of the genetic variation was found within populations. This implies either that the populations have originated from only a few common individuals or a high gene flow between populations. A relict population model is suggested to explain the observed pattern. Just after the last glaciation, S. angermanicum may have expanded its range when suitable habitat became available after the glacial ice retreated. Since then, habitats have vanished or fragmented and today only a few relict populations exist. This dioicous species has only once been reported with sporophytes in Scandinavia in modern time, but according to the genetic data, both the low level of linkage among loci and the estimated rate of recombination show evidence of sexual reproduction. However, reproduction may have been more frequent in the past. Based on the current knowledge of the species habitat requirements, life history, and the small population sizes, we conclude that the species will have an uncertain future in Sweden.