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Guggul (Commiphora wightii) is a critically endangered medicinal plant distributed in arid and semi-arid agroclimatic zones of Northern-west India. Information on genetic diversity of C. wightii using DNA markers even though reported is limited to Rajasthan and Haryana populations and that too without considering its reproductive behaviour. In the present study, we are reporting for the first time the genetic diversity vis-a-vis its reproductive behaviour by including more number of accessions from Gujarat, which is the only place in India where sexual populations are distributed. We used RAPD and ISSR markers since genome sequence information is lacking in the species. Twenty four RAPD primers and 16 ISSR primers amplified a total of 185 and 128 reproducible DNA fragments, respectively with fragment sizes ranged from 200 to 3000 bp. RAPD analysis showed higher polymorphism (80%) in comparison to ISSR (69%). Jaccardfs coefficient of similarity showed that pair-wise genetic similarity coefficients ranged from 46 to 98.3% in RAPD analysis, whereas it ranged from 47.8 to 98.6% in ISSR analysis. The results showed that the trend of genetic variation was not strictly correlated to the geographical locations, but was related to the reproductive behaviour of the populations. The diversity was somewhat low in Rajasthan populations where only apomictic populations are distributed. Populations of maximum genetic diversity along with sexual forms were found distributed in Gujarat populations, especially in Kutchh, Dwarka, Jamnagar and Porbandar populations. Hence the study indicated these areas as the original areas of the species distribution from where it was spread to the other parts of Gujarat and Rajasthan. (C) 2018 SAAB. Published by Elsevier B.V. All rights reserved.