Jojoba oil (JO) extracted from seeds has outstanding properties, including anti-inflammatory, antioxidant, and antibacterial activities, and can be stored forlong periodsof time. The unique properties of jojoba oil depend on its chemical composition; therefore, the effect of the jojoba genotype on the chemical properties and active components of the seed oil was evaluated in this study. Oil samples were collected from 15 elite Egyptian jojoba lines. The chemical composition, such as moisture, crude fiber, crude oil, ash, and crude protein of elite lines’ seeds was determined to investigate the variation among them based on the jojoba genotype. In addition, the iodine value was obtained to measure the degree of jojoba oil unsaturation, whereas the peroxide number was determined as an indicator of the damage level in jojoba oil. Fatty acid composition was studied to compare elite jojoba lines. Fatty acid profiles varied significantly depending on the jojoba genotype. Gadoleic acid exhibited the highest percentage value (67.85–75.50%) in the extracted jojoba oil, followed by erucic acid (12.60–14.81%) and oleic acid (7.86–10.99%). The iodine value, peroxide number, and fatty acid composition of the tested elite jojoba lines were compared withthose reported by the International Jojoba Export Council (IJEC). The results showed that the chemical properties of jojoba oils varied significantly, depending on the jojoba genotype.