The wide range of agroecosystems in Japan, from flooded paddy rice to upland wheat and soybean fields, presents distinct weed management challenges. With 4.3 million hectares of cultivated land in 2023, over half is dedicated to rice and about a quarter to upland crops. This chapter reviews weed management in rice, wheat, and soybean, presenting quantitative insights into weed flora and control strategies. Japan harbors a remarkable weed diversity, including 129 species in paddy fields and 583 species in upland fields; nearly half of the weeds in upland fields are alien plants. Intensive herbicide use—such as one-shot sulfonylurea applications in rice—has led to herbicide resistance in 23 weed species as of 2024 (20 in flooded rice fields). In wheat fields, Poaceae species, such as Alopecurus aequalis, Avena fatua, and Lolium multiflorum, have become problematic owing to the lack of registered post-emergence graminicides. The spread of alien weeds, such as Ipomoea spp. and Sicyos angulatus, poses increasing challenges in soybean fields. Given these pressures, Integrated Weed Management (IWM) is paramount, incorporating chemical controls, cultural controls (e.g., water management in rice, crop rotation, and competitive cultivars), and mechanical controls (e.g., tillage and autonomous weeder robots). A precautionary approach to preventing the spread of alien weeds is crucial because many of the troublesome weeds in upland fields are alien species. Effective quarantine measures under the Plant Protection Act by the Ministry of Agriculture, Forestry and Fisheries in Japan must be established. Field monitoring technologies, such as drone image capture and AI identification technologies, promise to improve early detection and control of weeds.