A. oryzae 3.042 (China) and A. oryzae RIB40 (Japan) used for soy sauce fermentation show some regional differences. We sequenced the genome of A. oryzae 3.042 and compared it to A. oryzae RIB40 in an attempt to understand why different features are shown by these two A. oryzae strains. We predict 11,399 protein-coding genes in A. oryzae 3.042. The genomes of these two A. oryzae strains are collinear revealed by MUMmer analysis, indicating that the differences are not obvious between them. Several strain-specific genes of two strains are identified by genome sequences' comparison, and they are classified into some groups, which have the relationship with cell growth, cellular response and regulation, resistance, energy metabolism, salt tolerance, and flavor formation. A. oryzae 3.042 showed stronger potential for mycelial growth and environmental stress resistance, such as the genes of chitinase and quinone reductase. Some genes unique to A. oryzae RIB40 were related to energy metabolism and salt tolerance, especially genes for Na(+) and K(+) transport, while others were associated with signal transduction and flavor formation. The genome sequence of A. oryzae 3.042 will facilitate the identification of the genetic basis of traits in A. oryzae 3.042, and accelerate our understanding of the different genetic traits of the two A. oryzae strains.