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This study investigates the variations in the chemical, genetic, and biological activity (antibacterial, antifungal, and antioxidant) profiles of thirteen populations of Ocimum kilimandscharicum Guerke (OK1-OK13) from India. Correlations between chemical composition and the biological activities of O. kilimandscharicum were assessed. The essential oils (EOs) of different populations, extracted by hydrodistillation process were characterised by gas chromatography-flame ionization detector (GC-FID) and gas chromatography-mass spectrometry (GC–MS). The antimicrobial activities of the EOs were evaluated by disc diffusion and micro dilution broth assays. The antioxidant activity of the EOs was determined by ferric reducing antioxidant power (FRAP) assay. The essential oil (EO) content varied significantly among the studied populations (0.15–0.93%). The EO analysis, and subsequent cluster and principal component analyses classified the populations in three distinct chemotypes, namely camphor (52.0–57.2%), linalool (65.2–91.0%), and phenylpropanoid/sesquiterpene. Amplification of genomic DNA using 20 inter simple sequence repeat (ISSR) primers yielded a total of 224 loci, out of which 210 loci were polymorphic in nature, representing 93.75% polymorphism. Pearson coefficient correlation ( r  = 0.32) suggesting low correlation between the distances obtained by molecular markers and EO compositions. The EO of population OK12 showed significant activity against Staphylococcus epidermidis , Enterococcus faecalis , and Staphylococcus aureus . However, EOs of populations OK11 and OK13 showed significant activity against Candida albicans (clinical isolate) and Candida albicans (ATCC), respectively. The EO of OK13 exhibited significant antioxidant activity. In-vitro safety evaluation study revealed that the EOs of most of the populations showed no significant toxicity against peritoneal macrophages cells. It is concluded that chemical and genetic profiles of O. kilimandscharicum varied considerably and these variations determined changes in its biological activities. The observations of this study could pave the way to optimize the use of O. kilimandscharicum populations in relation with its biological properties. [ABSTRACT FROM AUTHOR]