Alpha thalassemia is a genetic disorder of hemoglobin synthesis deletion or non-deletion mutation of the alpha-globin gene. Non-deletional mutations cause abnormalities in the structure of alpha-globin chain, creating an unstable variant of hemoglobin. Furthermore, hemoglobin Adana (HbAdana) and Constant Spring (HbCS) are common non-deletional alpha-thalassemia in Indonesia. However, compound heterozygosity cases of these types of mutations have rarely been reported. A 12-year-old boy is hospitalized with anemia, and complete blood count showed hemoglobin 9.1 g/dL, Mean Corpuscular Volume (MCV) 87.2 fl, and Mean Corpuscular Hemoglobin (MCH) 24.3 pg. On microcapillary hemoglobin electrophoresis examination, HbA 95.7%, HbA2 1.5%, and HbC 2.8% were obtained, and they led to the suspicion of HbCS. Furthermore, examination of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) found compound heterozygosity of HbAdana and HbCS. The genetic inheritance of compound heterozygosity Hb Adana and HbCS was discovered as the father was heterozygous for HbCS and the mother was heterozygous for Hb Adana. Generally, non-deletional mutations produce variant hemoglobin that is not clinically significant. However, when the point mutation occurs in essential amino acid residues, it will result in very unstable hemoglobin, which causes more serious clinical symptoms of hemolytic anemia than the deletional mutation. HbAdana and HbCS are variants of alpha thalassemia that are very unstable and can easily prevent hemolysis. Therefore, the compound heterozygosity of the two non-deletional mutations causes recurrent severe anemia. The compound heterozygosity of non-deletional alpha-thalassemia mutation is very rare, and microcapillary hemoglobin electrophoresis with molecular examinations are required for the diagnosis of HbAdana and HbCS.