Oryza nivara is the only annual AA-genome wild rice found in Asian. We performed its genome sequence was using Illumina GAIIx. We prepared the minimum tilling path using Bacterial Artificial Chromosome (BAC) end sequences and fingerprinting data, and picked up 2996 BAC clones for 12 chromosomes. About thirty BAC DNAs were used as one pool and then sequenced with a multiplex assay Illumina paired-end platform, pooling six or seven samples with index fragments into a single lane. With the assistance of Dr. Takeshi Itoh’s Bioinformatics Research Unit, we mapped the sequences of chromosomes 3 and 5 to the Nipponbare genome sequence using BWA software. Coverage of the O. nivara sequences against the Nipponbare genome was calculated from uniquely mapped sequences using the mpileup program implemented in SAMtools. The total consensus sequence lengths were 29,237,930 bp for the long arm of chromosome 3 and 55,528,267 bp for chromosome 5. The average depths of these chromosomes were 64x and 180x and their respective calculated coverages were 38.0% and 77.1%. We also used megablast to map the sequence contigs assembled by Velevt to the Nipponbare genome. These mapping results will be used to investigate the genome-wide sequence diversity between O. nivara and O. sativa. A de novo assembly and functional annotation of the unmapped sequences will help determine the unique genes that exist in the O. nivara genome.