In sturgeon aquaculture, the fish are sexed by an invasive surgical examination of the gonads. Development of a non-invasive procedure for sexing fish based on a molecular method is of special interest. In the present study a proteomics approach has been utilized to analyze a differential protein expression between mature male and female Persian sturgeon (Acipenser persicus) gonads. When comparing protein patterns on the 2-DE gels of the testis and ovary, 48 unique spots were distinguished in testis while only two spots were matchless in ovary. The spots were identified by MALDI-TOF/TOF analysis. The identified proteins are involved in metabolism and energy production, cell structure, transcription and translation, cell defense, signal transduction, transport, cell division, and none were directly linked to a sex-determining gene. The provided proteomics data could be considered as a starting base for subsequent studies focusing on the identification of proteins involved in sex determination and differentiation at different stages of gonadal maturation.