The species of Passiflora are widely used in folk medicine as mild sedatives and tranquilizers. P. alata and P. quadrangularis are distributed throughout South America, with widespread occurrence in Brazil and Colombia. Due to the difficulty in making a botanical distinction between these species, especially in the absence of flowers and fruits, the use of chemical markers for these plants offer an alternative method of identification. This work describes the isolation and identification of the major flavonoids and saponins from the leaves of P. alata and P. quadrangularis, as well as rapid and efficient HPLC-DAD methods for comparison of these compounds in both species. Vitexin derivatives are proposed as chemical markers in the identification of P. alata and P. quadrangularis and the detection of adulterations in raw material.