The presence of different weedy rice (WR) have already been reported in other areas of the Philippines. However, reports documenting its presence and phenotypic characteristics in Central Mindanao are not yet available. This study investigated the incidence, biology, and phenotypic characteristics of WR in Central Mindanao. Survey and collection were conducted in rice field areas of South Cotabato, North Cotabato, Sultan Kudarat, and Maguindanao from 2016–2017. Eight WR variants with distinct grain characteristics were identified and designated in 2016 DS (dry season); 24 variants in 2016 WS (wet season); 31 variants in 2017 DS; and 24 WR variants in 2017 WS. The most prevalent variants were WR-SuK3 (2016 WS), WR-SuK2 (2016 DS), WR-Min15 (2017DS), and WR-SuK3 (2017 WS). Germination test and characterization were conducted at the Philippine Rice Research Institute, Maligaya, Science City of Muñoz, Nueva Ecija. The collected WR variants had variable grain characteristics that affect grain quality and germinated earlier than cultivated rice, which makes WR more competitive. Under screenhouse conditions, all variants matured earlier and had better agronomic characteristics than cultivated rice (NSIC Rc 222). Identified agronomic characters of WR collected from Central Mindanao will be useful for advising control strategies to farmers.