Sickle cell disease is known to be very common in the Omani population, although data are limited concerning β-thalassemia (β-thal). We report the molecular background of 87 unrelated patients from the Sultanate of Oman, diagnosed with β-thal major (β-TM), β-thal intermedia (β-TI) or minor. Diagnosis was based on clinical and hematological data and confirmed by molecular analysis. We found 11 different β-thal determinants in our cohort, which consists of subjects from different regions of Oman. Six of these mutations have not been previously reported in the Omani population. The prevalence of α-thal single gene deletions (−α3.7 and −α4.2) in the same cohort was very high (58.3%). These data will contribute to the implementation of a country-wide service for early molecular detection of hemoglobinopathies and for providing genetic counseling following premarital screening.