Evolvulus alsinoides (L.) is an annually growing medicinal plant used in many popular systems as a source of traditional medicine. However, fresh plant material for medicinal uses and research purposes is critically unavailable year-round due to its short life cycle. A micropropagation method for E. alsinoides was developed, and its genetic diversity was described. Surface sterilized nodal explants were inoculated onto Murashige and Skoog (MS) medium supplemented with different plant growth regulators; the best response of multiple shoot induction was observed on MS media augmented with 5 μM kinetin (Kn) and 0.1 μM Indole-3-acetic acid (IAA), which gave a maximum number of 10.27 ± 0.0118 shoots. Further, the addition of 30 μM of adenine sulfate to the MS media enhanced shoot multiplication (18). The cloned shoots were accomplished to in vitro rooting on MS medium with 0.1 μM Indole-3-butyric acid (IBA) and 10 μM phloroglucinol, resulting in 16 healthy roots. The rooted plantlets were acclimatized in the shade house. The genetic stability of micropropagated plants was confirmed through molecular marker analysis. Gas chromatography-mass spectrometry (GC-MS) analysis of the tissues of clones revealed the contents of secondary metabolites. High-Performance Thin Layer Chromatography (HPTLC) revealed that squalene levels were highest in plants cultured in MS medium supplemented with adenine sulfate (378.89 ng/ 15 μl). The methods developed and defined are highly reproducible and can be used for commercial production of E. alsinoides valued for human health.