Object To preliminarily study the difference of proteins in the seed of spine date and the seed of Indian jujube. Methods Protein contents were measured with Kieldahl method. Amino acids constituting the protein were determined by means of acidolysis. The proteins were analyzed using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and capillary zone electrophoresis (CZE). Results Contents of proteins in the seed of spine date and the seed of Indian jujube were 36.13% and 41.58%, respectively. The content of valine and methionine in the seed of Indian jujube were significantly more than that in the seed of spine date remarkably, and the contents of other amino acids from the seed of spine date and seed of Indian jujube were similar. Their SDS-PAGE spectra showed that the seed of spine date contained a protein with molecular weight 39 800 and the seed of Indian jujube contained a protein with molecular weight 50 100 . In CZE spectra for the seed of spine date, there was a peak at the mobile time of 3.1 min and in CZE spectra from the seed of Indian jujube, there was a peak at the mobile time of 4.8 min. Conclusion Protein content in the seed of Indian jujube is more than that in the seed of spine date; The content of valine and methionine in the seed of Indian jujube is more than that in the seed of spine date remarkably. The spectra of SDS-PAGE and CZE for the seed of spine date are different from that for the seed of Indian jujube clearly.