Echinochloa species are among the most troublesome weeds inrice cultivation, and grow in a broad habitat range in Korea. Althoughvarious ecotypes of Echinochloa have been collected asgermplasm for future studies, it has been difficult to classify them due totheir high level of morphological similarity. This study was thus conductedto develop and investigate the phylogenetic relationships between 77 Echinochloa accessions with the use of 23 simplesequence repeat (SSR) markers and 24 morphological traits. Of 77 Echinochloa accessions, including 57 accessions fromKorea and 5 reference species, late watergrass was clearly clustered as adistinctive group from barnyardgrass and other Echinochloaspecies. In this analysis, we also identified core genetic and morphologicalmarkers that can be used for the future identification and classification of Echinochloa species. Five out of 23 SSR makers produceddistinctive bands that discriminate late watergrass from barnyardgrass andother Echinochloa species. Four morphological traits of thereproductive organs were the most influential contributors for classifying Echinochloa species. Although there was no clearconsensus generated in this study between SSR markers and morphologicaltrait analyses, our results support the potential use of the selected SSRmarkers and morphological traits in future studies of Echinochloa.