Aims: Thalassemia is one of the most prevalent inherited disorders in south China. However, there still has no comprehensive research on molecular characterisation of α-thalassemia and β-thalassemia in the Quanzhou region of Fujian province, a city with high incidence of thalassemia in Southeast China., Methods: A total of 11 668 cases were collected in Quanzhou region from January 2013 to June 2019. The deletions of α-thalassemia were detected by Gap-PCR, α-thalassemia and β-thalassemia mutations were detected by DNA reverse dot blot hybridisation. Rare thalassemia gene testing and DNA sequencing were performed to detect rare and novel thalassemia mutation for suspected rare thalassemia carriers., Results: Among 11 668 subjects, 4796 (41.10%) subjects were diagnosed with thalassemia. 3298 (28.27%) subjects were α-thalassemia carriers, 26 types of α-thalassemia mutations were identified, with the common α-thalassemia genotypes being -- SEA /αα (71.47%), -α 3.7 /αα (17.13%) and -α 4.2 /αα (3.49%). 1407 (12.06%) subjects were β-thalassemia carriers, 18 types of β-thalassemia mutations were identified. The common five genotypes of β-thalassemia were β IVS-II-654 /β N (36.53%), β CD41-42 /β N (30.28%), β CD17 /β N (17.13%), β CD26 /β N (5.12%) and β -28 /β N (4.62%). Additionally, 91 (0.78%) subjects with composite α-thalassemia and β-thalassemia were identified. Furthermore, 9 α-thalassemia and β-thalassemia gene mutations (CAP +40-43 (-AAAC), IVS-I-1 (G>T), IVS-I-5 (G>C), SEA-HPFH, CD53 (-T), CD37 (A>G), -90 (C>T), CD3 (T>C), -α 6.9 ) were identified for the first time in the region. Among them, CD53 (-T), CD37 (A>G) and -90 (C>T) mutations were identified for the first time in Fujian province. Moreover, CD3 (T>C), -α 6.9 mutations were first identified in Chinese individual., Conclusions: Quanzhou region of South China has high incidence of thalassemia mutations. In this study, several cases of rare thalassemia mutations have been identified, providing reference for clinical consultation. The completion of this study is of great significance to strengthen the prevention and control of thalassaemia in the Quanzhou region., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2020. No commercial re-use. See rights and permissions. Published by BMJ.)