In Ecuador, two species of Desmodium are used as traditional medicine. These are popularly known as “hierba del infante” and refer to D. adscendens and D. molliculum. The first species has a large base of information on its genetics and biological activity on which its traditional use is supported, while the second, D. molliculum, lacks this scientific information. This research aims to establish a base knowledge for the species D. molliculum: characterize the species genetically by obtaining the molecular DNA barcodes trnh-psbA, rbcL, matK, ITS1 and ITS2, evaluate its antioxidant effect and compare it with that of D. adscendens using the in vitro techniques of Folin-Ciocalteu, ABTS, DPPH and FRAP to assess its potential medicinal effect. De novo genetic DNA barcodes were obtained for the species D. molliculum and the phylogenetic analysis separated them from those obtained from D. adscendens, indicating that the analyzed species can be discriminated by DNA barcodes. In addition, the methanolic extracts of D. molliculum contain more than double the content of total polyphenols (30.1 ± 1.1 mg GAE/g dry plant) than those of D. adscendens (13.82 ± 0.74 mg AG/g dry plant) as well as better performance in all antioxidation assays. Additionally, this research established that the defatted extract of D. molliculum has the highest antioxidant activity in the ABTS (1.16 ± 0.001 mg TE/mg) and FRAP (0.39 ± 0.01 mg TE/mg) assays.