Taxonomic status of 14 Turkish endemic species and one variety of the genus Ebenius L. was analyzed using seed proteins and RAPD markers. These profiles were evaluated as characters to clarify the taxonomic relationships in the genus. A total number of 136 protein bands from all species, with molecular weight ranging between 116 kDa and 21 kDa were detected in SDS-PAGE electrophoregrams of the species studied. A total of 99 RAPD markers were generated by the 42 primers. The relative similarity between various taxa estimated by Jaccard's similarity index and clustered in UPGMA, is generally in accordance with taxonomic position. However, there are slightly different arrangements of these species from Flora of Turkey. Ebenus argentea Siehe ex Bornm. and Ebenus longipes Boiss. & Bal., are two different species in Flora of Turkey. However, this study revealed a close relationship between E. argentea and E. longipes. These taxa are clustered together and show genetic distance of 0.4% by SDS-PAGE and 33% by RAPD-PCR analysis. Ebenus plumosa Boiss. & Bal. var. plumosa has a seed protein banding profile very similar to Ebenus plumosa var. speciosa Hub.-Mor., genetic distance of 0.4%. In case of RAPD data, the genetic distance between two taxa is 44%.