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species (sp.) are gastrointestinal protozoan parasites with high prevalence rates worldwide. sp. show extensive genetic diversity with 17 different subtypes (STs) described to date. A few studies have investigated the prevalence and STs of sp. in Makkah, Saudi Arabia. Therefore, we aimed in this study to identify and characterize subtypes of sp. in the City of Makkah, Saudi Arabia. Stool samples were collected from 140 patients who presented to King Abdulaziz Hospital, Hera General Hospital and Modern Medical Center in Saudi Arabia. Different microscopic examination methods of patients' stools and molecular analyses (using primers targeting SSU rRNA gene) were performed to identify and characterize STs of sp. Our microscopic examination of stool samples showed that 96/140 patients (68.6%) had sp. infection. Clinical examination of infected patients revealed that 81 patients were symptomatic, whereas 15 were asymptomatic. Next, we isolated DNA from  sp.-positive stool samples followed by PCR amplification of small-subunit ribosomal RNA (SSU rRNA) gene and sequence analysis. Our sequence analysis showed that subtype 3 (ST3) was the most prevalent (53.13%) followed by subtype 1 (ST1) (45.83%), whereas subtype 2 (ST2) was the least prevalent (1.04%). Moreover, our results showed that all three STs resulted in more symptomatic than asymptomatic cases. Finally, we identified novel haplotypes which comprised of 8 ST3, 6 ST1, and one ST2 haplotypes. Our identification of several haplotypes in patients' stools confirms the genetic diversity of sp. and may explain the reported low host specificity and differential pathogenicity of sp. We believe that additional molecular epidemiological and genomic studies are needed to understand the prevalence and pathogenicity of different subtypes in humans and animal hosts.