Jojoba cultivation and production face the challenge of establishing ways to identify the sex at early stage of plant growth. The present study was carried out to identify sex of jojoba at the seedling stage under Sudan condition. Two DNA markers, ISSR (UBC807) and RAPD (OPG-5), were used for sex identification of jojoba genotypes: two known male and females genotypes and four unknown genotypes. ISSR marker, UBC807 was successfully amplified a unique male-specific band at 1200 bp, while RAPD marker, OPG-5 could not amplify a unique band within jojoba sex. The result clearly indicates that ISSR-UBC807 marker can be used for sex identification of jojoba at seedlings stage, a finding that could make the commercial cultivation and production of jojoba possible in Sudan.