Plants have proved to be the cure of many harmful diseases therefore, the demand of herbal medicines is increasing day by day. According to the previous research data Fagonia, a genus of 45 species is identified as a very potential medicinal plant against multiple diseases but poorly identified in Pakistan. As most of the biological research depends on the species identification and authentication, the sustainable method for the identification is now accepted as a molecular based method that employ DNA sequences as taxon ‘barcodes’ because taxonomic expertise are not serving the sole purpose. Therefore, we collect various Fagonia samples from different localities of Pakistan. Out of 12 samples, 7 were identified as F. indica, 3 as F. paulayana and 2 as F. bruguieri, and the potent species we have here in Pakistan is F. indica not F. cretica as they both are least similar. After that, the anti-oxidant, free radical scavenging and anti-fungal activities of methanol extracts of identified Fagonia species were checked. The best results were shown by F. indica then F. bruguieri and least were shown by F. paulayana.