Seeds from six selected jojoba genotypes were used in this study. Seed samples were analyzed for oil, protein, total carbohydrate, and simmondsin contents. The genetic relationships among jojoba genotypes were also determined. Highly significant differences among the genotypes were found for oil, protein, total carbohydrate and simmondsin contents. Genotype MD 8 recorded the highest oil content (54.95%), whereas genotype HD 6 had the lowest oil content (47.17%). However, the highest protein content (16.98%) and the highest carbohydrate value (33.97%) were found in genotype HB 6, which differed significantly from all the other genotypes. The significant variations in the studied characteristics observed among the genotypes might reflect, in part, their different genetic backgrounds. The inter-simple sequence repeat ISSR-derived data were evaluated to calculate the genetic similarity (ISSR-GS). The genetic similarity coefficient varied between 0.60 and 0.90. Cluster analysis was conducted to generate a dendogram to elucidate the relationships among jojoba genotypes. The dendogram generated using pooled ISSR data divided the jojoba genotypes into two main clusters. Genotypes HB8 and MD8 were found in the same sub-cluster using ISSR primers. These genotypes also had almost similar values for most chemical traits.