Echinochloa P. Beauv. is an important genus because many of its species are weeds infesting most paddy fields, which can reduce the rice grain production by up to 80%. A controversy exists about the taxonomy of the genus due to the high level of morphological variations found in these species. Cyhalofop-butyl, an aryloxyphenoxy-propionate herbicide, is used to control Echinochloa spp. in paddy fields, although differences in susceptibility were found between different Echinochloa species. E. colona was highly susceptible [ED50= 34 g of active ingredient (ai) ha(-1)]; very similar results were obtained with the remaining species. By contrast, E. oryzicola (170 g of ai ha(-1)) was less sensitive, with the herbicide symptoms appearing later. Because of this differential susceptibility, morphological and molecular studies were carried out. A morphological study, using 21 characters both quantitative and qualitative of spikelets and seedlings, was capable of clearly distinguishing closely related E. crus-galli plants (two populations), E. muricata and E. crus-pavonis, and E. oryzicola, E. utilis, and E. colona species. The resolution of Echinochloa species at the molecular level, based on RAPD analyses, was fairly consistent with morphological analysis results. Among the 60 primers screened, 21 primers exhibited polymorphic bands and produced a total of 136 RAPD markers. Of all the amplified fragments, 90 were found to be polymorphic. E. oryzicola and E. colona were clearly separated, and the RAPD analyses showed that both E. crus-galli populations were 100% related and 51% related to E. utilis, whereas E. crus-pavonis and E. muricata (73% similarity) appeared as being clearly separated from this group.