Jojoba (Simmondsia chinensis [Link] Schneider) is a crop of high economic interest that is grown for the exceptional quality of its seed oil. We have taken advantage of the large variation commonly shown by ribosomal DNA (rDNA) in many plant species to assess the genetic diversity between clones and among individuals in jojoba. The variation of rDNA was analyzed with the use of a homologous 1.7-kbp probe generated by PCR and a 20-mer oligonucleotide probe targeting, respectively, the 17S and 25S coding regions. The multiple-step ladder obtained with the BamH I-EcoR I restriction fragment containing the intergenic spacer (IGS) was the best indicator of variation in length of rDNA unit. In addition to variations observed among selected clones, significant differences in the relative proportion of length variants were seen among individuals grown from seeds of unknown origin.