Heading date (flowering time) is one of the most important traits for the adaptation of rice to different environmental area. However, it is limited that genetic analyses have been performed under short day conditions. To find novel QTLs for heading date under short day (SD) conditions, we developed F2 population crossed between early heading cultivar, Nipponbare, and late heading line (BIL55) which derived from the back cross inbred lines crossed between Nipponbare and Kasalath. To conduct QTL-seq, bulked DNA samples from extreme early and extreme late heading were prepared. The extreme early bulk DNA was separated into two categories based on the order of heading date, and the extreme late one was separated into four categories. The parents and six F2 bulked sample were genome-widely re-sequenced.