||Aspergillus oryzae has a very long history of use in the production of traditional fermented foods and beverages. Comparison of the genomes of the A. oryzae 3.042 and A. oryzae A100-8 which diverged by the N+ ion implantation mutagenesis reveals considerable similarities. However, some differences between gene-sequences were observed such as: SNPs, nucleotide deletion or insertion; some of these may reflect the ability of A. oryzae to secrete proteases and explain the mechanism of mycelium growth. Both A. oryzae 3.042 and A. oryzae A100-8 have a strikingly larger proportion of genes encoding proteases, 50% of these are extracellular enzymes. Transcriptional analysis of the two strains during three different growth processes provided further insights into the genes and pathways involved in secreting proteases and cell growth. This has led to the development of the different levels of functional genomic analysis the transcriptome, proteome, and metabolism, as well as high-throughput approaches for determining phenotypes.