Salvia connivens Epling, Lamiaceae, is an annual herbaceous plant used as a traditional medicine in Mexico for the treatment of diarrhea, which out can be caused by bacterial, viral, and protozoal infections, as well as toxins mainly. Mexican medicinal plants with anti-diarrheic activity represent a source of potential antiprotozoal agents. The phytochemical isolation of the constituents of an acetone-soluble extract led to the isolation of the known flavonoids: eupatorin, cirsiliol, and nuchensin. The structures of these compounds were elucidated by the analysis of their NMR and MS data. Nuchensin displayed potent antiprotozoal activity against Entamoeba histolytica (IC 50 0.072 ± 0.006 μM) and Giardia lamblia (IC 50 0.118 ± 0.006 μM), which was comparable to metronidazole.