Banana bunchy top virus (BBTV) is a destructive viral disease in many countries including Egypt. It causes severe economic losses because infected banana plants produce no fruit. -The tissue culture approach was used to permit the recovery of BBTV-free plantlets, genetic stability followed by chemotherapy and early screening to facilitate the efficient production of virus-free plantlets. Results demonstrated that application of 10,20,30,40 mg/L thiouracil in vitro gave an 85,72,35,20  survival and 60, 83, 91 and 95.5% BBTV-free plantlets ,respectively. Furthermore, the obtained virus free micropropagated plantlets were subjected to DAS-ELISA detection. Tissue culture-derived genetic stability banana plants and virus tested plants were screened by RAPD- PCR. Only two RAPD primers (among 10 tested) were chosen as producing polymorphic DNA bands differentiating the investigated micropropagated plants. Based on DNA markers, the genetic stability between micropropagated plants were estimated. The morphological variations were recorded in shoots of micropropagated clones more than healthy clone. The developed RAPD profiles of different micropropagated clones were untypical to that of the healthy clones. The phylogenetic free recorded that the plantlets derived from healthy and sanitary (10 mg/L thiouracil) plants showed close similarity within the first group while sanitary (20 mg/L) second group and sanitary (30 and 40 mg/L) plants third group showed 70 and35% similarity with first group. The results demonstrated that application of 10 to 20 mg/L thiouracil in vitro gave survival plantlets higher than30 and 40 mg/L thiouracil.