Echinochloa species are among the most troublesome weeds in rice cultivation, and grow in a broad habitat range in Korea. Although various ecotypes of Echinochloa have been collected as germplasm for future studies, it has been difficult to classify them due to their high level of morphological similarity. This study was thus conducted to develop and investigate the phylogenetic relationships between 77 Echinochloa accessions with the use of 23 simple sequence repeat (SSR) markers and 24 morphological traits. Of 77 Echinochloa accessions, including 57 accessions from Korea and 5 reference species, late watergrass was clearly clustered as a distinctive group from barnyardgrass and other Echinochloa species. In this analysis, we also identified core genetic and morphological markers that can be used for the future identification and classification of Echinochloa species. Five out of 23 SSR makers produced distinctive bands that discriminate late watergrass from barnyardgrass and other Echinochloa species. Four morphological traits of the reproductive organs were the most influential contributors for classifying Echinochloa species. Although there was no clear consensus generated in this study between SSR markers and morphological trait analyses, our results support the potential use of the selected SSR markers and morphological traits in future studies of Echinochloa.