Boiling meat in meatball making process can cause DNA degradation. This study aims at determining the effect of boiling temperature on beef and pork DNA detection in meatball samples using Real Time Polymerase Chain Reaction (RT-PCR). DNA of beef, pork, beef meatballs, pork meatballs and beef-pork meatballs boiled at 8° C, 90° C, and 100° C were isolated using the Wizard Genomic DNA Purification Kit and amplified using the RT-PCR. The result has shown DNA of beef meatball, pork meatball, and beef-pork meatball samples heated to 80 o C, 90° C, 100° C can be amplified. Here, the Cycle threshold (Ct) value of the beef meatball, pork meatball, and beef-pork meatball samples heated to 80 °C, 90 °C, 100 °C is significantly different from that of unheated beef and pork (p <0.05). However, there is no significant difference in the Ct value of the beef meatball, pork meatball, and beef-pork meatball samples heated to 80 ° C, 90 ° C, 100 ° C (p≥0.05). It can be concluded that the beef and pork DNA in meatballs boiled at 80 o C to 100 o C is detectable by the RT-PCR.