IR64 is a mega rice variety with high-yield and high-quality and was grown on over 10 million hectares in 2000. IR64 has been replaced by modern varieties in most growing areas. Since modern varieties are mostly progenies or relatives of IR64, the genetic studies of IR64 is valuable for rice functional genomics. However, chromosome-level genome sequences of IR64 have not been available yet. Therefore, in this study, we sequenced the IR64 genome using synthetic long reads obtained by linked-read sequencing and ultra-long reads obtained by nanopore sequencing.