Abstract: Aloe vera L. (Aloe barbadensis Miller) is an ayurvedic, xerophytic, succulent, medicinal plant commonly known as Aloe vera and it is used worldwide in drug and cosmetic industry. In the present investigation, genetic diversity in 12 elite accessions of Aloe vera, collected from different geographical regions of India, were evaluated using Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR) markers. Molecular polymorphism was 71.8% with 64 RAPD primers and 80.9% with 25 ISSR primers indicating high level of genetic variation among the accessions and the mantel test revealed positive correlation between the two marker systems. Dendrogram was constructed based on pair wise genetic similarities and two-dimensional principal coordinate analysis using data from RAPD and ISSR marker systems showed similar clustering pattern and separated accessions into two major groups. The accession IC111279 and IC111272 appeared to be more divergent with 14.3% similarity, while high similarity of 84.7% was recorded between IC111280 and IC111279. The study clearly indicates that RAPD and ISSR marker profiles were best-suitable for assessing genetic relationships among Aloe vera accessions.