Generally, DNA of crime scene evidence is obtained from body fluids such as blood, semen and saliva. The detection and identification of body fluids are the most important step in forensic investigation. Especially, the determination of semen is very significant in case of sexual violence. Prostatic acid phosphatase test as the presumptive test for searching presence of semen is commonly used because of its convenience and cost/time-effectiveness. In this study, we tried to figure out the effect of AP reagent on DNA analysis according to the time dividing into two groups, control and experimental (AP reagent reaction). The degree of DNA condition was evaluated by the DNA concentration, degradation index and STR analysis. The result of degradation index of experimental group is higher than the control group. Also, in STR analysis, peak height and peak height ratio (PHR) of experimental group is lower than the control group increasing the effect of AP reagent on DNA analysis over time. Therefore, we confirmed that it is necessary to be cautious using the AP reagent on the whole of forensic evidence for high-quality DNA analysis.