Microscopic examination is known as the "gold standard" for laboratory confirmation of malaria. The technique is proven to be relatively simple, quick and inexpensive. However, this method has a downside when it comes to being sensitive. Besides, trained manpower and special certificates are required to carry on the diagnosis. The research was conducted to test on the ability of quantitative Polymerase Chain Reaction (qPCR) to quantify the number of P. berghei parasites that were injected into mice. The research is coupled with the examination of probiotic influence affecting the parasite growth. Both microscopic and molecular techniques were compared based on observing the number of P. berghei reflected per day basis by each technique. The research showed that the lowest detectable parasites caught by molecular technique are 0.05 parasites/µL (50 parasites/mL). The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) generated by qPCR technique is 93%, 100%, 97% and 100%, respectively. Willcoxon statistical tests were also performed to conclude the significant differences between the two types of diagnosis (p>0.770). However, qPCR technique proved to be able to detect the parasite a day in advance on the positive control group and treatment group than microscopic. It can be inferred that the molecular technique (qPCR) can replace the microscopic technique for the diagnosis of malaria.