In this study, we investigated interspecific variations in Sections Dendrobrychis, Hymenobrychis, Heliobrychis, Onobrychis of genus Onobrychis by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) technique and RAPD. Total eight species collected from different regions of Turkey were studied for the analysis of seed storage protein profiles and RAPD profile to examine their relationship. Electrophoretic data were documented by using a gel documentation system and analysed by using Quantity 1 -D analysis software and also the dendrogram was formed in UPGAMA. The sections Dendrobrychis, Heliobrychis, Hymenobrychis, Onobrychis of genus Onobrychis were firstly determined by morphological classification. In addition to RAPD and the seed protein of these species belonging to these sections were clustered together. The formed dendrogram from SDS-PAGE analysis showed that all studied species constituted two clusters. The first one consisted of O. huetiana subs. bornmuelleri, O. huetiana, O. montana, O. stenostachya and O. atropatana var. grandiflora and the second one O. viciifolia, O. hajastana and O. cornuta. The dendrogram realized from the RAPD markers grouped the Onobrychis spp. into three major clusters. Cluster 1 included O. huetiana subs. bornmuelleri, O. viciifolia, O. huetiana, O. atropatana var. grandiflora, O. montana and O. cornuta, Cluster 2 included O. stenostachya and Cluster 3 O. hajastana.