Within a significant genetic diversity consisting of 7 genotypes of Giardia intestinalis; assemblage A and B genotypes have been suggested to have different host specificities and variable pathogenicity in humans. Assemblages are highly variable with regard to the genetic features of each genotype. A total of 89 fecal samples were collected from patients who sought medical consultation for abdominal pain in the West Bank, Palestine. Giardia positive samples were assessed microscopically and where genotyped to assemblage level by direct sequencing and subcloning for both triosephosphate isomerase and β-giardin gene markers. G. intestinalis were detected in 12 samples; 9 samples were belonging to assemblage A and 3 samples were belonging to assemblage B. A single genotype was identified from all assemblage A samples, whereas 2 to 4 subgenotypes were confirmed in each of assemblage B samples. No mixed genotypes (inter-assemblages) were found in any sample. This study revealed the contrasting genetic diversity that supports the separate-species notion for assemblage A and B genotypes; it also highlights the need to investigate assemblage B genotype more thoroughly, as has been the case for assemblage A genotype.

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