Red clover (Trifolium pratense) is a highly polymorphic cross-pollinating legume species from Fabaceae family. It is important as fodder for livestock, as it improves nutritional value of feed. Red clover is important in agriculture, especially because it is able to perform symbiotic nitrogen fixation by Rhizobium sp. Slovenian plant gene bank (SPGB) stores 114 red clover accessions. The aim of the work was to determine genetic and morphological diversity of red clover accessions from SPGB and selected varieties and to determine concentration and distribution of red clover isoflavones by high pressure liquid chromatography and mass spectrometry. Using microsatellite markers, high diversity within individual genetic resources (86,6 %) was detected, while diversity between different genetic resources (13,4 %) was small. Fifteen morphological traits were evaluated. Differences of isoflavone concentration and differences between different preservation methods after harvest were observed. Total isoflavone concentrations for ‘Poljanka’ variety were the highest when drying at 105 °C for 20 minutes and at 65 °C for 5 hours in flowering phenophase. The content of genistein, prunetin and ononin varied significantly between genotypes. Information on genetic and morphological diversity and content of isoflavones in Slovenian genetic resources is important for further breeding of new red clover varieties.