According to the Global Strategy for Plant Conservation, 75% of endangered species should be preserved in ex situ collections till 2020. The genus Liparis has a lot of recognised taxons, but only one species, Liparis loeselii (L.) Rich., grows in Europe. L. loeselii is a rare and endangered orchid species occurring in Europe. In Latvia L. loeselii is classified as the third category of endangered and protected species. To develop the best conservation strategy, the knowledge concerning the genetic differences of protected plants in a particular area is crucial. For this purpose, the genetic diversity of L. loeselii populations from different Latvian habitats was tested. The inter-retrotransposon amplified polymorphism method (iPBS) was used for population genetic diversity evolution. In total, 54 accessions from nine habitats were collected and analysed. L. loeselii leaves have a high content of phenols that reduce the quality of extracted DNA. It was found that the percentage of polymorph loci varied among the populations of L. loeselii growing in different habitats; some of the populations were genetically homogeneous. The genetic diversity levels of L. loeselii populations are related with the population age and the growing conditions.