The goals of this study are to compare different gene expressions for Penicillium oxalicum wild type strain (WT), Hat1 deletion strain (?Hat1) and AmyR deletion strain (?AmyR) in 2% starch as carbon sources. The correlation analysis results between the various samples showed that the gene expression levels of the wild strain and the ?Hat1 strain were significantly different, and the gene expression levels between ?AmyR and the wild strain were also significantly different. The deletion of Hat1 significantly up-regulates the expression levels of amylase genes of Penicillium oxalicum, and the absence of AmyR can significantly down-regulate the expression level of amylase genes genes, indicating that Hat1 and AmyR can cause a difference in amylase synthesis by affecting the expression of amylase genes. The information provided by this study indicates that Hat1 and AmyR functions are necessary for the amylase activity of Penicillium oxalicum. Overall design: Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain, Hat1 deletion mutant strains and AmyR deletion strain in 18h in modifeid Mendal’s medium with 2% starch as carbon sources. Three replicates were included for each samples.