The present study has been planned to investigate the extent to which seed proteins and peptide mapping may be used as evidences to discuss the position of T. cylindracea Desv. and T. Polyceratia (L.) Trautv. To achieve this objective two outgroups (reference species): Trigonella foenum-graecum L. and Medicago sativa L., represent the type species for each genus were used. Each species was considered as an operational taxonomic unit (OTU) for the purpose of classification and ordination. The bands from 1D-SDS-PAGE or the spots from 2D-peptide mapping were scored as 0 representing absence and 1 representing presence, and employed in the analysis by using NTSYS-pc computer and PAST programs. Cluster analysis and PCA using the protein data from the two different techniques demonstrated that the similarity between T. polyceratia and M. sativa is more than that to T. foenum-graecum. The present paper accepts the transfer of T. polyceratia to Medicago and recommends further studies for T. cylindracea.