Weedy rice is one of the most dominant and competitive weed species found throughout rice planting areas worldwide. In Malaysia, a combination of agricultural practices such as direct seeding and shared use of machinery has contributed to the rapid proliferation of weedy rice across paddy fields in recent decades. Here, we report on the morphological characterization of weedy rice populations and inferred origin(s) of different morphotypes present in Peninsular Malaysia. Eight weedy rice morphotypes were distinguished based on a combination of traits such as awn presence/absence and hull color, from 193 accessions collected in 17 locations. Results showed a high proportion of awnless accessions (strawhull-, intermediate strawhull-, and brownhull-colored morphotypes, together composing 65% of sampled accessions), with awned accessions represented by strawhull, brownhull, and blackhull forms. Clustering and PCA analyses revealed four major clusters: (1) O. rufipogon and the majority of awned, blackhull, and brownhull—suggestive of a type of weedy rice originating from wild Oryza populations; (2) elite indica cultivar rice and the majority of strawhull weeds—supporting a previous proposal that weedy rice from Malaysia mainly evolved from indirect selection on cultivars for easy-shattering feral forms; (3) the majority of brownhull; and (4) a mixture of other weedy morphotypes—potentially reflecting multiple origins and subsequent admixture. The combination of key morphological descriptors will be useful for advising farmers appropriately in strategies for controlling the spread of weedy rice, including periodic manual weeding to reduce buildup of the seed bank in the fields.