Blastocystis species are zoonotic protist commonly found in animals and humans. To date, 17 subtypes of Blastocystis have been identified, nine of which have been isolated from humans. This study aimed to determine the frequency of Blastocystis subtypes in patients diagnosed with urticaria and to explore the relationship between patient symptoms and Blastocystis subtypes. Stool samples from 100 urticaria patients and 100 healthy volunteers were analyzed for the presence of Blastocystis spp. using direct microscopic examination with the native–Lugol method and the subtypes were identified through PCR and sequencing techniques. A questionnaire was administered to the patient group to gather information on symptoms, socio–economic status, and hygiene practices. Blastocystis spp. was detected in 9% (9/100) of the urticaria patients and 5% (5/100) of the control group. The distribution of Blastocystis subtypes in the patient group was as follows: ST2 (n = 4, 44.4%), ST3 (n = 3, 33.3%), ST1 (n = 1, 11.1%), and ST4 (n = 1, 11.1%). In the control group, the distribution was ST3 (n = 2, 40%), ST1 (n = 2, 40%), and ST2 (n = 1, 20%). Regarding the relationship between symptoms and Blastocystis subtypes, 8 of 9 (88.9%) Blastocystis–positive patients reported rash, 7 (77.8%) experienced itching, 6 (66.7%) had fever, 3 (33.3%) experienced swelling, and 1 (11.1%) reported abdominal pain. Notably, bloating and abdominal pain were observed exclusively in patients with ST2. It is crucial to highlight the elevated prevalence of Blastocystis in areas where livestock farming is prevalent and the zoonotic cycle in the transmission of the parasite. While limited studies have suggested a correlation between Blastocystis subtypes and urticaria, the high prevalence of ST2 in urticaria patients may indicate its significant role in pathogenicity. The data derived from the patient questionnaire highlight a notable association between ST2 and symptoms such as bloating and abdominal pain, warranting further investigation.