Hemoglobin (Hb) gene disorders are common inherited diseases in Taiwan. The α- and β-thalassemias are among the well-known Hb diseases in this area. We reviewed abnormal hematological data in 3578 cases, identified between 1998 and 2009, as being at-risk for α-thalassemia (α-thal) (n = 1909; 53.3%), β-thal (n = 743; 20.8%), non-α, β-thal (n = 872; 24.4%), and α-thal combined with β-thal (n = 54; 1.5%), and collected fetal blood samples for prenatal testing. The most common types of α(0)- and α(+)-thal were the SEA (Southeast Asian) deletion and the -α(3.7) rightward deletion, with frequencies of 87.79 and 4.85%, respectively. The frequency of the IVS-II-654 (C>T) mutation, the most common β-thal mutation in this region, was 38.6%. Hb E [β26(B8)Glu→Lys, GAG>AAG] was found to be the most common Hb variant, and it was concluded that Hb Tak [β147 (+AC)], Hb G -Taichung (also known as Hb Q-Thailand) [α74(EF3)Asp→His, GAC>CAC (α1)], Hb Owari [α121(H4)Val→Met (GTG>ATG)], and Hb Phnom Penh [α117(GH5)Phe-Ile-α118(H1)Thr (α1)] were very rare. The results of this study provide a primary reference for designing a locally relevant antenatal diagnostic test for controlling the spread of thalassemia.