Background and objectives: This study aimed to characterize the spectrum of β-thalassemia mutations and haplotypes of sickle cell anemia in Beja tribes and other minor groups living in Port Sudan, Sudan. Methods: This descriptive cross-sectional study was carried out from March 2011 to July 2013. Overall, 209 anemic patients were screened for hemoglobinopathy by capillary electrophoresis. The subjects were genotyped for β-thalassemia mutation by amplified refractory mutation system and for sickle cell haplotype by restriction-fragment length polymorphism. Results: Of the 209 patients, 29 (13.87%) showed the typical-88(C→T) βthalassemia mutation and 27 (12.91%) had sickle cell anemia, of whom 15 (55.6%) were heterozygous AS and 12 (44.4%) were homozygous SS. Based on results of the restrictionfragment length polymorphism; all subjects were with Benin haplotype (Benin/Benin). Conclusion: Based on the results of this study, it is recommended to perform a potential carrier screening for the-88 (C→T) mutation and sickle cell Benin haplotype by DNA analysis.