Weedy rice is one of the most dominant and competitive weed species foundthroughout rice planting areas worldwide. In Malaysia, a combination ofagricultural practices such as direct seeding and shared use of machineryhas contributed to the rapid proliferation of weedy rice across paddy fieldsin recent decades. Here, we report on the morphological characterization ofweedy rice populations and inferred origin(s) of different morphotypespresent in Peninsular Malaysia. Eight weedy rice morphotypes weredistinguished based on a combination of traits such as awn presence/absenceand hull color, from 193 accessions collected in 17 locations. Resultsshowed a high proportion of awnless accessions (strawhull-, intermediatestrawhull-, and brownhull-colored morphotypes, together composing 65% ofsampled accessions), with awned accessions represented by strawhull,brownhull, and blackhull forms. Clustering and PCA analyses revealed fourmajor clusters: (1) O. rufipogon and the majority of awned,blackhull, and brownhull—suggestive of a type of weedy rice originating fromwild Oryza populations; (2) elite indicacultivar rice and the majority of strawhull weeds—supporting a previousproposal that weedy rice from Malaysia mainly evolved from indirectselection on cultivars for easy-shattering feral forms; (3) the majority ofbrownhull; and (4) a mixture of other weedy morphotypes—potentiallyreflecting multiple origins and subsequent admixture. The combination of keymorphological descriptors will be useful for advising farmers appropriatelyin strategies for controlling the spread of weedy rice, including periodicmanual weeding to reduce buildup of the seed bank in the fields.