Some tropical species—such as the domesticated Xanthosoma sagittifolium (L.) Schott (Taioba) and Colocasia esculenta (L.) Schott (Taro)—have similar phenotypic characteristics, especially in the shape and color of the leaves and petioles which generate uncertainty in their identification for use in human food. This study aimed to analyze the morphological and molecular characteristics of X. sagittifolium and C. esculenta that may help in the popular and scientific identification of these species. The principal morphological characteristics of X. sagittifolium were as follows: leaves with subcoriaceous textures, basal insertion of the petiole, green pseudo-stem in the basal portion with exudate being white and the presence of two collector veins. Distinctive morphological characteristics of C. esculenta were as follows: leaves with velvety textures, peltate insertion of the petiole, pink pseudo-stem in the basal portion with pink exudate and presence of one collector vein. The morphological characteristics that can be used to distinguish Taioba from Taro are the basal petiole insertion of the first, against the petiole insertion near the center of the blade of the latter. Molecular analyses using eight Inter-Simple Sequence Repeat (ISSR) molecular markers simultaneously showed distinctive fingerprints for each of the species. These results contribute to the proper identification of the species used as a food source.