Weedy rice is a notorious weed in the rice agroecosystem. Its infestation has caused significant economic loss in many rice-production countries, including Malaysia. In Malaysia, weedy rice consists of a genetic admixture of cultivated and wild traits, resulting in a highly competitive ability against cultivated rice for resources. The morphology and genetic plasticity of weedy rice provide several adaptive advantages, enabling it to thrive in rice agroecosystems and become a serious weed infesting Malaysian rice granaries. Previous strategies in combating weedy rice have often been less effective since weedy rice is easily adapted to a wide range of environments. In this review, we address the weedy rice issue in Malaysia and the progress of weedy rice studies. A future direction on weedy rice research via omics study is also discussed to propose solutions for improvement in weed control, good agronomic practices, and food security.