This study was carried out with the objective of determining the optimum reaction conditions for the polymerase chain reaction (PCR) in Musa germplasm. DNA was extracted from young leaves and purified. Amplification reactions were carried out with different concentrations of taq DNA polymerase, MgCl2 as well as template DNA for the PCR. For the RAPD analysis of Musa germplasm. The ideal concentration of the thermostable polymerases, MgCl2 as well as the template DNA for the PCR was defined. As a result, the optimum concentrations were 3 mM for MgCl2 , 20 ng for template DNA and 0.70u for taq DNA polymerase. These were the concentrations that yielded reproduceable amplification products in different replications with Kenyan Musa germplasm.