The inflorescence and spikelet structural units of rice significantly impact grain development. Among the grasses, the sterile lemma represents a unique spikelet organ exclusive to rice. As most studies on sterile lemma genes primarily focus on Asian cultivated rice (Oryza sativa L.), genes influencing the sterile lemma phenotype in African rice remain unreported. This study identified lsl3, a gene located on the short arm of chromosome 7 that controls the sterile lemma length in African rice. The key mutation of lsl3, leading to long sterile lemmas in African rice, was discovered and differed from that in Asian rice. The investigation of lsl3 not only provides a reference for the molecular evolution of cultivated rice in Africa but also offers new evidence supporting the parallel domestication of rice and the independent origin of Oryza glaberrima.