Ocimum (Lamiaceae) species are commercially important medicinal and aromatic plants with proven efficacy in Unani and Ayurvedic systems of medicine. Their essential oils are highly valued in fragrance, flavoring and pharmaceutical industry. Several researchers have observed complexity in taxonomy and the estimate of total number of species in Ocimum genus. In this study, chemical variability among different accessions of Ocimum genus was determined. Essential oils were extracted and their constituents were analyzed using gas chromatography. Caryophyllene, alpha-caryophyllene and linalool appear to be prominent markers in Ocimum. We have also developed new EST derived microsatellite markers, transferable across different species of Ocimum genus and validated them in a limited set of Ocimum accessions.