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Jojoba, Simmondsia chinensis (Link) Schneider, a desert shrub belongs to family Simmondsiaceae. In the current study the cumulative molecular and phytochemical approach is used to investigate 18 different accessions of Simmondsia chinensis collected from AJORP (Association of Rajasthan for Jojoba Plantation and Research Project), Rajasthan (Jaipur). The focus of this study was the correlation of molecular and phytochemical characters at the intraspecific level. DNA fingerprinting of jojoba accessions was performed using RAPD markers along with the fatty acid profiling of its oil using GC-MS technique. Both molecular analysis and biochemical fingerprinting cumulatively revealed a significant level of variability among accessions. Ten major fatty acids were found in all the accessions, out of them oleic acid (OA) was in high concentration. Further OA content of individual accession was correlated with RAPD analysis data. High OA containing accessions were grouped together in a single cluster. On the basis of our results, it can be concluded that three accessions which were grouped in a single cluster 2a (82-18,48-25 and 58-5) are the best. Thus, these accessions could be better candidates for different commercial applications. Our data strongly suggest that cumulative approach (molecular and biochemical) proved to be best for accessing the relationship between different accessions of jojoba in future breeding programs. (C) 2016 Elsevier B.V. All rights reserved.