This study was aimed to investigate the prevalence and genotype distribution of heterozygotes in beta-thalassemia combining deletional alpha-thalassemia by using molecular detection and haematological methods. Three common deletions of alpha-thalassemia were detected by using gap-PCR. The mutations of beta-thalassemia were identified by using PCR with reverse dot blot hybridization. The routine analysis of blood cells was carried out. The results indicated that 15 cases from the 81 beta-thalassemia traits were found to be the compound heterozygosity for beta-thalassemia and alpha-thalassemia with 9 different types of gene defects with 18.52% detection rate. There were 6 cases (7.41%) of beta-thalassemia heterozygote combining alpha-thalassemia-1 gene (--(SEA)/alphaalpha), 8 cases (9.88%) combining with alpha-thalassemia-2 gene including 6 (7.41%) right ward deletion (-alpha(3.7)/alphaalpha) and 2 (2.47%) left ward deletion (-alpha(4.2)/alphaalpha), and 1 case (1.23%) combining deletional HbH gene (--(SEA)/-alpha(3.7)). No significant differences were found between beta-thalassemia heterozygotes combining deletional alpha-thalassemia and pure beta-thalassemia in all RBC parameters. It is concluded that the incidence of beta-thalassemia heterozygotes combining with deletional alpha-thalassemia is frequent in Wuzhou city. The hematological analysis can not give specificity for diagnosing these dual heterozygotes. Gap-PCR as a routine method for thalassemia screening has the advantages in reducing the possibility of failing to detect the combining heterozygosity for beta-thalassemia and alpha-thalassemia. It is more useful for genetic counselling and prenatal diagnosis of this disease.