Background Thalassemia is a group of inherited hemoglobic disorders resulting from defects in the synthesis of one or more of the hemoglobin chains, which is one of the most prevalent inherited disorders in southern China. Only few studies reported the molecular characterization of alpha- and beta-Thalassemia in Hubei Province in the central of China. Methods A total of 4889 clinically suspected cases of thalassemia were analyzed by Gap-PCR, PCR-based reverse dot blot (RDB). Results 1706 (33.8%) subjects harbored thalassemia mutations, including 539 (11.0%) subjects with alpha-thalassemia, 1140 (23.3%) subjects with beta-thalassemia mutations, and 25 (0.51%) subjects with both alpha- and beta-thalassemia mutations. Seven genotypes of alpha-thalassemia mutations and 29 genotypes of beta-thalassemia mutations were characterized. --(SEA)/alpha alpha (66.05%), -alpha(3.7)/alpha alpha (24.12%), and -alpha(4.2)/alpha alpha (3.71%) accounted for 93.88% of the alpha-thalassemia mutations. beta IVS-II-654/beta N, beta CD41-42/beta N, beta CD17/beta N, beta CD27-28/beta N, beta CD71-72/beta N, beta - 28/beta N, beta - 29/beta N, beta CD43/beta N, beta E/beta N, accounting for 96.40% of all beta-thalassemia genotypes. Furthermore, mean corpuscular volume (MCV) and mean corpuscular Hb (MCH) were sensitive markers for both beta-thalassemia and alpha-thalassemia with --(SEA)/alpha alpha, but not -alpha(3.7)/alpha alpha and -alpha(4.2)/alpha alpha. Conclusions: Our data indicated great heterogeneity and extensive spectrum of thalassemias in Hubei province of China.