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The molecular markers namely random amplified polymorphic DNA, amplified fragment length polymorphism, sequence-characterized amplified region, inter simple sequence repeats, simple sequence repeats and single-nucleotide polymorphism, etc. have been successfully used for genetic diversity studies in <em>J. curcas</em>. The assessment of genetic variations among Jatropha germplasms using molecular markers show the presence of high genetic diversity for the Central and South American regions and insignificant genetic variation from Asia and Africa. The use of molecular markers for the assessment of phylogenetic relationships among different Jatropha species has been restricted only to the well adapted and acclimatized species in India. The significant genetic variability in the genus Jatropha for vegetative and floral traits for seed oil content, productivity, toxicity (phorbol esters, curcin), fatty acid profiles, etc. has been studied in the past decade using molecular markers. Genetic enhancement of Jatropha through conventional breeding and interspecific gene transfer can be attempted by exploiting the diverse genetic resource form <em>J. curcas</em> and their wild species. This review focuses on the importance and use of molecular markers towards studying diversity analysis in <em>J. curcas </em>growing at different areas.