Entamoeba species infect humans and non-human primates, raising concerns associated with potential zoonotic transmission. Therefore, the prevalence of human Entamoeba infections is crucial for its management in areas, where macaques exhibit high infection rates. Previously, we demonstrated prevalent E. nuttalli infections in rhesus macaques in Kathmandu, Nepal. In this study, we surveyed Entamoeba infection among 185 schoolchildren from two schools visited by wild rhesus macaques to assess the risk of transmission. PCR-based screening for Entamoeba species identified E. coli in 13 % and E. dispar in 0.5 % of the human stool samples. However, E. nuttalli and E. chattoni infections, prevalent in macaques, were not detected in human samples. This suggests that Entamoeba spp. are not transmitted through macaques in the school environment. We surveyed the rhesus macaques living in the temple near schools as well as the rhesus and Assam macaques inhabiting Shivapri Nagarjun National Park, Kathmandu. Among the 49 macaque stool samples, E. chattoni, E. coli, E. nuttalli, and E. dispar were detected in 92 %, 86 %, 41 %, and 18 % of the samples, respectively. Notably, E. dispar infections in macaques were mostly prevalent in the temple. A sample isolated from Nagarujun showed an identical genotype at two tRNA-linked short tandem repeat loci to that of E. dispar isolated from humans, suggesting potential transmission from humans to macaques. Genotypic analysis of cultured E. nuttalli strains obtained from the macaques colonizing three locations demonstrated that the geographical distance rather than differences in macaque species played a crucial role in the genetic diversity of the parasites. The phylogenetic tree of E. nuttalli strains, including the previously isolated strains, reflected the geographical distribution of the isolation sites. This study sheds light on the intricate dynamics of Entamoeba transmission and genetic diversity in macaques and humans.