The use of seed proteins in the evaluation of genetic diversity is cost effective and less time consuming. Water and salt-soluble proteins from the seeds of Citrus species: C reticulata, C. aurantifolia, C grandis, C. sinensis, C. limon, and C. microcarpa were extracted and variations in electrophoretic profiles were determined. Finely grounded seeds were homogenized in 50 mM Tris buffer, pH = 7.0, centrifuged at 14,000 rpm for 10 minutes at 4ºC, and the supernate collected as the water-soluble fraction. The pellet was resuspended in 50mM Tris buffer, pH = 7.0 in 150 mM NaCl, homogenized, then centrifuged at 14,000 rpm for 10 minutes at 4ºC, and the supernate collected as the salt-soluble fraction. Samples were analyzed using SDS PAGE. Nine protein bands were found common to all samples and six bands were used as genetic markers in the water-soluble fractions. A dendrogram was constructed for the water-soluble proteins. In the salt-soluble fraction, ten protein bands were found to be common to all samples and five bands were concluded to be genetic markers. C.reticulata and C.sinensis possessed identical water and salt soluble protein profiles and C. grandis were found to be most distinct among the samples.