Enteric parasitic infections are a leading cause of diarrheal disease and malnutrition in low- and middle-income countries like Kenya. Among the most prevalent protozoan pathogens in children are and species. However, data on their genetic diversity, co-occurrence, and variability in Kenya remain limited. This study investigated the genetic diversity of spp. and spp. in children aged 10 years and below in Kiambu County, Kenya. A total of 550 stool samples were analyzed for enteric parasites using formal-ether concentration and Modified Ziehl-Neelsen staining. Genomic DNA was extracted from microscopy-positive samples, and species-specific nested polymerase chain reaction was performed to genotype spp. using the 18S ribosomal RNA gene. For and spp., nested PCR and sequencing targeted the , triose phosphate isomerase, and 60-kDa glycoprotein genes, respectively. Microscopy detected spp. (29.6 %, 163/550), (14.6 %, 80/550), and spp. (1.3 %, 7/550). PCR analysis identified (3.3 %, 18/550), (3.8 %, 21/550), (1.6 %, 9/550), (13.1 %, 72/550), and (1.5 %, 8/550). Sequence analysis of the and genes identified assemblages A (20/50) and B (30/50). All assemblage A isolates were classified as sub-assemblage AII (20/20), while assemblage B isolates were further subdivided into sub-assemblages BIII (21/30) and BIV (9/30). All isolates were identified as , with subtypes IbA9G3 (5/6) and IeA11G3T3 (1/6). Microscopy results revealed a significant association between spp. and spp. with both age groups and study sites. by PCR and by microscopy showed significant differences between study sites. Additionally, the distribution of assemblages A and B, along with sub-assemblages AII, BIII, and BIV, differed significantly between the study sites. Among these, only sub-assemblage BIV showed a significant association with age groups. The detection of alongside related spp. underscores the importance of molecular diagnostics for accurate amoebiasis management and epidemiological surveillance. Additionally, the identification of sub-assemblages AII, BIII, and BIV, as well as subtypes, suggests anthroponotic transmission, emphasizing the need for improved sanitation and public health interventions.