Hypericum perforatum L. (St John’s Wort) is a medicinal plant that produces pharmaceutically important compounds with antidepressive and anticancer activities. H. perforatum is a facultative apomictic species as it has the ability to reproduce with multiple reproduction mechanisms affecting genetic structure and chemical composition of the plants. The objective of this study was to determine nuclear DNA contents and ploidy levels of H. perforatum L. plants growing naturally in the flora of Turkey. The seeds of 39 Hypericum perforatum L. accessions collected from 23 different locations in Turkey were used in the study. Nuclear DNA contents of three different seedlings for each of the 39 H. perforatum accessions were determined using flow cytometry. Based on the results of flow cytometric analysis, nuclear DNA contents of the accessions varied between 0.8-2.57 pg 2C-1. Nuclear DNA content differences observed among H. perforatum accessions were statistically significant (P<0.01) and the Duncan test revealed that the accessions formed three clearly distinguishable main groups. Mean nuclear DNA contents of each group were 0.80 pg 2C-1, 1.58 pg 2C-1 (1.36-1.73 pg 2C-1) and 2.38 pg 2C-1 (2.15-2.57 pg 2C-1). Ploidy levels were determined by correlating nuclear DNA content of accessions with the number of their mitotic chromosomes by counting chromosome number of one plant from each group. Findings suggest that H. perforatum accessions used in this study had the following three different ploidy levels: diploid, tetraploid and hexaploid. The percentages of diploid, tetraploid and hexaploid accessions were 2.2, 86.4 and 11.4% respectively.