Acute Mylenoid Leukemia is a cancer of the blood or bone marrow and is characterized by an abnormal proliferation of blood cells, usually white blood cells. A number of genes are involved in regulating heamatopoiesis, and thereby affecting the susceptibility to Leukemia. Among them is the gene which is responsible for FMS like-tyrosine kinase-3 (FLT3). FLT3 is important protein that plays a role in cell proliferation and differentiation. In this work A 3D model of FLT3 was generated using 1RJB (Chain A: Crystal structure of Juxtamembrane domain of FLT3) as template with the help of Modeller7v7. With the aid of the molecular mechanics and molecular dynamics methods, the final model is obtained and is further assessed by Procheck and Verify 3D graph programs, which showed that the final refined model is reliable. After energy minimization we compared the 3D structure of FLT3 with template. We identified 21 genes coding for FLT3 and their locus regions. Multiple alignment and phylogenetic analysis showed that the total FLT3 family proteins formed 4 branches. From the result we identified mutations within FLT3 domain region.