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<p>Abstract</p> <p>Background</p> <p>The glutamate dehydrogenase gene (<it>gdh</it>) is one of the most popular and useful genetic markers for the genotypic analysis of <it>Giardia duodenalis </it>(syn. <it>G. lamblia</it>, <it>G. intestinalis</it>), the protozoan that widely causes enteric disease in humans. To determine the distribution of genotypes of <it>G. duodenalis </it>in Thai populations and to investigate the extent of sequence variation at this locus, 42 fecal samples were collected from 3 regions of Thailand i.e., Central, Northern, and Eastern regions. All specimens were analyzed using PCR-based genotyping and recombinant subcloning methods.</p> <p>Results</p> <p>The results showed that the prevalence of assemblages A and B among these populations was approximately equal, 20 (47.6%) and 22 (52.4%), respectively. Sequence analysis revealed that the nucleotide diversity of assemblage B was significantly greater than that in assemblage A. Among all assemblage B positive specimens, the allelic sequence divergence within isolates was detected. Nine isolates showed mixed alleles, ranged from three to nine distinct alleles per isolate. Statistical analysis demonstrated the occurrence of genetic recombination within subassemblages BIII and BIV was likely.</p> <p>Conclusion</p> <p>This study supports increasing evidence that <it>G. duodenalis </it>has the potential for genetic exchange.</p>