Hassawi rice (Oryza sativa L.) is a landrace adapted to climate of Eastern Saudi Arabia. Hassawi rice is characterized by wide adaptability to soil salinity and drought. However, it bears some undesired characteristics such as susceptibility for lodging, delayed maturity, and photoperiod sensitivity. In this study, we sequence the genomes of two Hassawi cultivars using next generation sequencing platforms (both 454 and SOLiD and minimal coverage of 40X per genome). One cultivar, Hassawi_I, is the wild type originated from subspecies indica and the other Hassawi_II is a hybrid between the Hassawi_I and IR1112. Using an improved reference-guided assembly method, we achieved high-quality assemblies that contain a limited numbers of gaps. Compared to the genome sequences of indica (9311) and japonica (Niponbare) as well as plant genome sequences, we confirmed the phylogenetic relationship of Hassawi rice among cultivars of Oryza sativa L. Moreover, we analyzed conserve genes, SNP/Indel distributions, structural variations, and chromosomal rearrangements, and our results provide a better understanding of the origin of Hassawi rice in the Middle East and clues and tools for improving the productivity and quality of this aboriginal rice cultivar.