The banana is the most important fruit in Egypt. Banana bunchy top disease, caused by the banana bunchy top virus (BBTV), is one of the most damaging infections on banana plantations, resulting in significant crop losses. The current study was conducted to characterize the incidence of banana bunchy top disease (BBTD) and to study the molecular characteristics of BBTV from banana plantations in Ismailia. This study was conducted during the period 2019-2021 in three locations (Abu-Suwayr, El Tal-El kabir and Fayed) in Ismailia Governorate. The occurrence of BBTV was initially studied using visual inspection of external virus symptoms. TAS-ELISA, PCR and nucleic acid hybridization were used to detect the virus. Further molecular characterization of BBTV was performed based on Rolling Circle Amplification (RCA) and nucleotide sequencing. BBTD incidences ranging from 3.33 to 5.14% were observed in two localities Abu-Suwayr and El Tal-El kabir.  While a relatively low incidence of 1.48% was observed in Fayed. Our results showed that the BBTD incidence is directly related to the percentage of winged aphids inside the aphid colonies regardless the percentage of the aphid's occurrence. The PCR product (973 bp) of BBTV- component 3 (DNA-S) was used for the creation of a non-radioactive Dig labeled- DNA probe for further use for BBTV detection using dot blot and  Southern blot hybridization. The sequence comparison analysis of DNA-S component showed that the present Ismailia isolate (BBTV-3F) shared nucleotide identity 98.4%- 91.9 % with three isolates from Qalubya Egypt and shared 97.9% nt identity with east African isolates (Rwanda and Malawi). The phylogenetic analysis revealed that the DNA- component 3 (DNA-S) of the BBTV-3F isolate from Ismailia belongs to the South Pacific group (SPG) and is markedly separated from those of the Asian group (AG). This study is important for monitoring and early detection of BBTV threats and for rapid eradication of infected plants before the virus spreads and settles in a new area