Background: Understanding the genetics underlying the heritable subphenotypes of sickle cell anemia, specific to each population, would be prognostically useful and could inform personalized therapeutics. The objective of this study was to describe the genetic modulators of sickle cell disease in a cohort of pediatric patients followed up in Mayotte. Methods: In this retrospective cohort study, clinical and biological data, collected between 1 January 2007 and 31 December 2017, in children younger than 18 years, were considered for the analysis. Results: We included 185 children with 72 % SS, 16 % Sβ0-thalassemia and 12 % Sβ+ thalassemia. The mean age was 9.5 years; 10 % of patients were lost to follow up. The Bantu haplotype was associated with an increase in hospitalizations and transfusions. The alpha-thalassemic mutation was associated with a decrease of hemolysis biological parameters (anemia, reticulocytes), and less cerebral vasculopathy. The Single Nucleotide Polymorphisms BCL11A rs4671393, BCL11A rs11886868, BCL11A rs1427407 and HMIP rs9399137 were associated with the group of children with HbF> 10%. The survival analysis without occurrence of cerebral vasculopathy showed that the group of patients with HbF> 10% presented a significant risk of early onset of cerebral vasculopathy. Conclusions: The most remarkable result of our study was the association of SNPs with the phenotypic groups that we aimed to determine. BCL11A rs4671393, BCL11A rs11886868, BCL11A rs1427407 and HMIP rs9399137 were correlated with the HbF group> 10%, which presents a higher risk of cerebral vasculopathy and would be oriented towards the hemolytic sub-phenotype.