The present study aims to: 1) identify acid sulfate soil (ASS)-tolerant rice varieties from the genetic stock of Korean rice (Oryza sativa L.) varieties under ASS conditions; 2) to evaluate their yield performance, and elucidate the physiological mechanism for ASS tolerance with the identified tolerant varieties. Two hundred sixty-six rice varieties were screened for ASS tolerance, and we identified two japonica-indica hybrid varieties, Geumgang (GG) and Pungsan (PS), as having high tolerance under ASS paddy conditions (pH 3). We first conducted a yield trial of GG and PS grown in Wagner pots to determine their potential yields under ASS conditions. A yield trial under paddy field condition followed. In the pot experiment, the ASS-tolerant varieties, GG and PS, showed significantly higher yields than PT-1, which is a local reference variety in mildly improved soil pH conditions (pH 4.1-4.6). Al and Fe content in GG and PS were significantly lower than that of PT-1, so there might be some mechanism that inhibits the absorption of toxic metal ions in the tolerant varieties. In the paddy conditions, the grain yields more than $5;t;ha^{-1}$ of the two tolerant varieties under mildly improved soil pH condition were significantly higher than PT-1. Dry matter weights of above ground parts also showed the same trend as grain yield. The study demonstrated that the ASS-tolerant japonica-indica rice varieties with high yielding potential could contribute to the improvement of rice yield in ASS regions, and will be good materials for the development of acid soil-tolerant rice varieties.