Abstract: The factors influencing RAPD Analysis, including the concentration of DNA template, Mg2+, dNTP, primers, Taq polymerase, denaturing time, Thermal cycles and annealing temperature in fruit flies were studied. An optimal PCR system for RAPD in fruit flies has been found: in 25μl reaction solution, contained 80ng DNA template, 2.0mMMg2+, 0.2 mMdNTP, 0.5μMprimers, 1U Taq polymerase.The amplification program was devised: 94℃ for 3min; denaturing at 94℃ for 45sec, primer annealing at 36℃ for 1min, extension at 72℃ for 2min, 40cyclesm, at last extension at 72℃ for 10min.