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Background: Hemoglobinopathy and thalassemia are prevalent genetic disorders throughout the world. Beta thalassemia is one of these disorders with high prevalence in Iran, especially in Khuzestan province. In this study, the rate of different mutations in β-globin gene for prenatal diagnosis in fetal samples was evaluated. Materials and methods: In this experimental pilot study, 316 fetal samples (chorionic villus or amniotic fluid) suspicious to hemoglobin disorders were enrolled. Afterwards, DNA was extracted and PCR and DNA sequencing were used for evaluation of different mutations in β-globin gene. Results: Amongst 316 samples evaluated for prenatal diagnosis, 180 cases (56.8%) were carrying at least one mutated gene of β-thalassemia. In addition, results showed that CD 36-37 (- T) and IVS II-1 (G>A) polymorphisms are the most prevalent polymorphisms of β-thalassemia in Ahvaz city with 13.9 % and 10.1% rates, respectively. Conclusion: Using molecular tests for prenatal diagnosis is considered an efficient approach for reducing the birth of children with hemoglobinopathy and identification of prevalent mutations in each region