Screening of the endophyte microbes in cinchona stems of C. Ledgeriana and C. pubescens that could produce alkaloids has been carried out. The screening was done using Potato Dextrose Broth A and B media for obtaining the optimum condition for the alkaloids productions by endophyte microbes. Qualitative and quantitative analysis of the alkaloids were carried out using thin layer chromatography and high performance liquid chromatography. The result show that two endophytic fungi (LMC-19 and LMC-29) produced alkaloid compounds. In Potato Dextrose Broth and B media LMC-19 and LMC-29 produced quinine while in B medium LMC-29 could also produce cinchonine.