Introduction: : Baluran National Park (BNP) is one of the oldest national parks in Indonesia. Due to its natural beauty, BNP is also the highest number of tourists in Indonesia. Macaca fascicularis is one of the species that has a high population abundance in several park locations. Several species of Entamoeba have been reported as pathogenic and non-pathogenic to humans and Non-human primates (NHP). The aim of this research was to detect gen 18 SSU rDNA of Entamoeba spp in long-tailed macaque at Baluran National Park. Methods: A total 100 faecal samples of Macaca fascicularis taken from BNP, Indonesia. Samples were purified with sugar flotation methods, and extracted the DNA using DNAzol. For molecular identification of Entamoeba spp, using primer pairs Entamoeba-specific primers, including Entam1 (5-GTT GAT CCT GCC AGT ATT ATA TG-3) and Entam2 (5-CAC TAT TGG AGC TGG AAT TAC-3), have been designed by Verweij et al. Amplification is carried out 5 min at 95° C; 40 denaturation cycles of 30 s, 95° C; 30 s for annealing at 57° C, and 30 s for extension at 72° C, with a final step of 2 min at 72°C. Results: The prevalence of Entamoeba spp. based on PCR examination was 53% (53/100). The PCR products from Entamoeba spp. isolates from Macaca fascicularis produced bands of around 600 bp with 2% agarose gel electrophoresis. Conclusion: there was a high prevalence of Entamoeba spp in Macaca fascicularis in BNP, and E. coli were identified with 18 SSU rDNA genes.