Ceiba pentandra (Kapok trees) serve the purpose of drug which we know as tribal medicine. Based on research before, most of secondary metabolites were found in the stem and stem water of C. pentandra which could produce antimicrobial compounds against Staphylococcus aureus and Escherichia coli. Nevertheless, little is known about the diversity of endophytic microorganisms inhabit the stem and stem water of C. pentandra and their potential to produce bioactive compounds. The purpose of this work was to know the diversity of endophytic microorganisms inhabited the stem and stem water of C. pentandra. The microbes were isolated from the stem and stem water of C. pentandra. The endophytes were characterized based on the morphology appearance of the microbial endophytes microscopical and macroscopical. From the samples of stem water, 278 isolates of the microbial endophytes grew at NA medium and 31-257 isolates at PDA medium whereas from stem, 4 isolates of the microbial endophytes grew at NA medium and 2 isolates at PDA medium. When identified morphologically and biochemically, only 7 colonies at stem water and 5 colonies at stem had showed identifiable differences. Among the microbial group the most frequently in endophytic association with stem water may it be khamir. Meanwhile, bacteria was the most frequently in endophytic association with stem. This research indicated that culturable endophytes in the stem and stem
water of C. pentandra were very diverse. Microbial endophytes are suggested as an outstanding source of bioactive natural products that could be useful for medicines.