Thalassemia is an inherited blood disorder and traditionally considered more prevalent in Southern China. However, with increased migration and intermarriage, more and more thalassemia carriers had been reported in Northern China. The lack of screening for thalassemia carriers may also result in missed diagnosis in Northern China. Additionally, thalassemia carriers are usually asymptomatic or mild anemia, but their anemia can get worse during pregnancy. Iron deficiency anemia (IDA) is also one of the causes of anemia during pregnancy. In particular, both IDA and thalassemia are characterized by microcytic hypochromic anemia. The overlap of symptoms and the presence of thalassemia carriers with IDA may lead to misdiagnosis. In this study, long-read sequencing based approach termed comprehensive analysis of thalassemia alleles (CATSA) had been performed for 244 pregnant women in Northern China whose results of routine blood examinations were abnormal. As a result, 16.39 % (40/244) of the anemic pregnant women carried at least one mutation of thalassemia. One Hb H patient and a rare α-globin gene triplication combined with β-thalassemia were also identified. Of the 44 thalassemia variants detected, the -α