Seed storage proteins were studied by using SDS-PAGE in 14 populations of two Alhagi species, namely A. graecorum Boiss. And A. pseudalhagi (M. B.) Desv. In total 11 protein bands were obtained among which, bands 1,2,4,5, 7, 9 and 10 were common in all the taxa studied while band 3 is specific in Mehran population of A. graecorum. Cluster analysis of protein data revealed that such data may not be useful in differentiating the two Alhagi species, however they can be used in revealing the inter-population variation.