Hemoglobinopathies are common inherited diseases in southern China. The aim of the present study is to analyze the hematologic and molecular features of hemoglobinopathies in Shanghai, in order to provide a reference data for screening hemoglobinopathies. A total of 1029 samples were studied using High Performance Liquid Chromatography (HPLC) on the Bio-Rad Variant II HPLC system. GAP-PCR and reverse dot blot (RDB) were used to detect globin gene mutation or deletion. DNA sequencings for Alpha Globin gene (HBA1/A2) and Beta Globin gene (HBB) were simultaneously performed. We found that among 1029 samples, beta-thalassemia was the predominant type of hemoglobinopathy (39.16%). Six (0.58%) cases of beta-thalassemia major and 397 (38.58%) cases of beta-thalassemia carriers were identified. Among those beta-thalassemia samples, a total of 19 mutations were found, among which the β 654 /β N mutation (168/1029,16.33%) was the main type, followed by the β 41-42 /β N mutation (118/1029,11.47%). There were 136 (13.22%) cases of alpha-thalassemia (silent carrier & minor) and 39 (3.79%) cases of HbH disease. A total of 10 gene mutations were found in the alpha-thalassemia samples, among which the main genotype of deletion α-thalassemia was --SEA /αα(119/1029,11.56%), while non-deletion α-thalassemia was uncommon in our report(2/1129,0.19%) both of which was α WS α/αα. The main genotype of HbH was --SEA /-α 3.7 (28/1029, 2.72%). In 13 (1.26%) cases of αβ-thalassemia, with a total of 9 genotypes were found, among which the more common genotypes were -α 3.7 / β 654 , --SEA/β 41-42 and --SEA/β 17 . The ten main structural hemoglobin variants of 14 (1.36%) cases were Hb E