The family Pyrolaceae is represented in Bulgaria by six species, belonging to three genera. The viewpoints for the taxonomical position of the species in this family are not clearly unilateral. The aim of this study is to find molecular markers, allowing the objectively differentiation of the genera in this family, without use of morphological characters. Three species of the family were examined, representing the tree genera distributed in Bulgaria: Moneses uniflora (L.) A.Gray, Orthilia secunda (L.) House and Pyrola minor L. DNA was isolated from leafs and amplified via PCR reactions using 4 primers. The results were processed using cluster analysis and non-metric multidimensional scalling. The consequent cladogram, obtained by the mean euclidean distances, displayed grouping of the samples by genera, independently of their locality. The independent multitudes confirm the accuracy of the method for determination of the species in Pyrolaceae.