Background: Thalassemia is one of the most prevalent inherited single gene diseases. Prevention of β-thalassemia through prenatal diagnosis is the one of the most effective and direct approach to control the spread of this life-threatening disease. This study aims to determine the prenatal diagnosis of α-thalassemia and β-thalassemia in 3049 families among eighteen regions of Hainan Province using molecular diagnosis.Methods: This study enrolled a total of 3049 couples and their fetuses at The First Affiliated Hospital of Hainan Medical University from January 2004 to March 2020. Genomic DNA was extracted from peripheral blood of the couples and villus, amniotic fluid, or fetal cord blood of fetuses. DNA-based diagnosis was performed using polymerase chain reaction. Results: Here, the most commonly detected mutation of α-thalassemia was a South-East Asian deletion (31.53%), followed by –α4.2/αα (11.15%), –α3.7/αα (11.02%). The most common mutation for β-thalassemia was CD41/42, followed by -28, accounting for 30.27% and 2.56%, respectively. The regions with the highest prevalence were the coastal regions and the regions with the lowest prevalence were Wenchang, Lingao and Ding’an. We also examined thalassemia gene mutations in Han people and other minority groups and found that the most common gene mutations in different ethnic were not homogeneous. Prenatal diagnosis showed 556 normal, 118 α-thalassemia hydrops and 161 β-thalassemia major fetuses. Conclusion: Our findings provide important information for clinical genetic counseling of prenatal diagnosis for thalassemia major in Hainan Province.