<p>Hainan is an area with high prevalence of thalassemia and complex genetic background. There are few studies on the prevalence and genotype of thalassemia in different ethnic groups of infertility patients in Hainan province. The aim of our study was to explore the prevalence and genotype of thalassemia among infertile individuals in Hainan Province. Thalassemia genotypes were determined using gap-PCR and PCR-RBD in 13,856 infertile individuals in our study. Among them, 3458 (24.96%) were diagnosed as thalassemia carriers. In Li ethnic group, 649 (75.12%) were diagnosed as thalassemia carriers, which significantly higher than Han (21.62%) and other ethnicities (22.09%). As the molecular spectrum of thalassemia, the most common α-thalassemia genotype among Han and other ethnicities was -α^3.7/αα, while among Li ethnic group was -α^4.2/αα. For β-thalassemia, the most common genotype among Han and Li ethnic groups was β^{41−42&#xa0;M}/βN, while both β^{41−42&#xa0;M}/βN and β^17M/βN were common genotype in other ethnic groups. In αβ-complex thalassemia, the most common genotype among the Han ethnic group was -α^3.7/αα &amp; β^{41−42&#xa0;M} /βN, followed by -α^4.2/αα &amp; β^{41−42&#xa0;M} /βN in the Li ethnic group, and αα^WS/αα &amp; β^{41−42&#xa0;M} /βN and -α^4.2/αα &amp; β^{41−42&#xa0;M} /β^17M were common in other ethnic groups. Compare with reproductive age population, the infertile population in our study exhibits a notably higher prevalence of α-thalassemia carriers, particularly those with the silent type. This study reveals the genetic epidemiology of thalassemia in the region, providing a scientific basis for targeted health interventions, screening programs, and genetic counseling for infertile population in Hainan Province.</p>