β-thalassemia is one of the most prevalent inherited hemoglobin disorders. Compound heterozygotes or homozygous mutations of the β-globin chain gene account for severe cases of β-thalassemia that require lifelong transfusion, and make it necessary to identify β-thalassemia carries for prenatal diagnosis. The increase in hemoglobin A2 (HbA2) level is the most significant parameter in the identification of β-thalassemia carriers. HbA2, composing of two α chains and two δ chains, is a minor component of the hemoglobin present in normal adult red blood cells, accounting for about 2.5% of the total hemoglobin in healthy individuals. However, HbA2 level is also elevated in some pregnant women. This study aimed to evaluate the value of HbA2 level in the screening of pregnant women with β-thalassemia trait. Pregnant and non-pregnant women were randomly recruited who attended the prenatal care or diagnosis at our hospital located in Guangdong, a province in South China. Hemoglobin capillary electrophoresis was performed on high performance liquid chromatography to measure HbA2 levels in blood. The β-globin gene mutations were detected by the PCR-reverse dot-blot assay, and some were verified by direct sequencing. Pregnant women (n = 96) and non-pregnant women (n = 114) with normal HbA2 level (< 3.5%) had no β-thalassemia mutation. In contrast, pregnant women (n = 55) and non-pregnant women (n = 85) with elevated HbA2 level (≥ 3.5%) are β-thalassemia carriers. In conclusion, HbA2 level is a good marker for screening β-thalassemia trait in pregnant women in South China population.