Pichia pastoris (P. pastoris) has been used extensively in the production of various recombinant proteins of different origins. However, the molecular mechanisms of recombinant gene expression in this yeast have not been adequately studied. Microarray-based transcriptomic analyses have pointed out the differences in transcriptional levels of beta-Lactamase (bla) between control strain and recombinant a-amylase (Amy) or human Interleukin-2 (IL-2) strains. To clarify the relationship between the expression of bla and recombinant Amy/IL-2 genes in P. pastoris strains, the transcription levels of those genes need to be evaluated more precisely and detailed with real-time PCR Real-time PCR technique was used with mRNA samples extracted from recombinant Amy/IL-2 and control strains at 0, 6, 12, 24, 48 h of fermentation after the first methanol induction. Transcription levels of bla in different samples were compared using the average threshold cycles of three different fermentation batches and relative quantification method. The results shown that there were great differences between recombinant Amy/IL-2 strains with control strains at every time points, but there was no significant difference when comparing recombinant Amy strain with IL-2 strain. The transcription level of bla in recombinant Amy/IL-2 strains reached maximum value of 45-fold of control strain at time 12 h time point. In addition, there were also small differences when comparing expression levels in different time points. The difference was more than two-folds between different points of the control strain, whereas there was difference between the 24 h point and 48 h point of the IL-2 strain. Others comparisons had the less-than-two value.