Abstract <p>Thalassemia is one of the most prevalent inherited hemolytic diseases. This study aimed to characterize thalassemia mutations and provide an epidemiological basis for prevention and control of the disorder in Putian. A total of 6,380 individuals were enrolled in Putian from March 2017 to February 2025. Common thalassemia mutations were screened by polymerase chain reaction-flow-through hybridization, while rare thalassemia gene variants were detected by gel electrophoresis and DNA sequencing.&#xa0;2,264 cases (35.49%) were confirmed as thalassemia, including 1,418 cases of α-thalassemia, 807 cases of β-thalassemia, and 39 cases of co-inheritance of α- and β-thalassemia. Among the 31 α-thalassemia genotypes identified, deletions were predominant, including --^SEA/αα (71.93%), -α^3.7/αα (14.03%), and --^SEA/-α^3.7 (2.61%), with --^SEA being the most frequent α-thalassemia allele. Of the 21 detected β-thalassemia genotypes, the most common were β^{IVS−II−654}/β^N (48.76%), β^CD41–42/β^N (27.35%), and β^CD17/β^N (10.40%), with β^{IVS−II−654} being the most frequent β-thalassemia allele. In addition, 18 distinct genotypes of co-inheritance of α- and β-thalassemia were identified. Population migration has introduced new thalassemia genotypes to Putian. It was also found that the carrier rate of thalassemia genes in the infertile population of Putian was twice that of the local general population.Compared to other global regions, the thalassemia gene mutation spectrum in Putian exhibits unique genotypic diversity and population heterogeneity; moreover, the prevalence of thalassemia is higher in the local infertile population than that in the general population. These findings will provide valuable insights for thalassemia prevention and genetic counseling in this region.</p>