Some species of the genus Echinochloa are troublesome weeds in rice fields. The taxonomy of this genus leads to confusion in many cases due to its great morphological diversity. Because of the differential sensitivity to the herbicide quinclorac shown by Echinochloa spp., it was necessary to assess the botanical and molecular characterization of this weed. Echinochloa colonum, E. oryzoides, and E. oryzicola were very susceptible to quinclorac treatment; by contrast, E. crus-galli and E. hispidula showed some degree of natural tolerance. Physiological and molecular results agreed with the botanical classification of the genus Echinochloa in Flora Europea. The importance of these results is due to yield losses produced by the infestation of Echinochloa and the need for a strategy for Echinochloa management depending on the distribution of the Echinochloa species.