Several banana cultivars are grown in all types of farming systems, which Egyptians use in a mature way due to their nutritional value, and banana bunchy top virus (BBTV) contributive pathogen of Banana Bunchy Top Disease (BBTD) remains to be the furthermost devastating pathogen, which is threatening production in major banana growing areas. The current study was planned to determine the genetic variations of some banana cultivars using some molecular tools. Genetic variations of three BBTV-infected banana cultivars (Edward Cavendish, Maghrabi and Williams) collected from Qalyubia Governorate compared to healthy banana ones determined by using two molecular techniques, i.e., start codon targeted (SCoT) and/or SDS-PAGE. SCoT technique was also used to determine DNA fingerprinting of Maghrabi plant cultivar grown under different climate conditions. Results showed that, quantum of genetic variation in genome of similar variety whatsoever healthy or infected with BBTV was highest probable in Maghrabi cultivar (6-9%) followed by Williams cultivar (3-6%) and the lowest was Edward Cavendish cultivar (3-4%). It was proved that identities percentage between samples of two regions of Qalyubia Governorate exceeds 70% and that they both found in same cluster, while identities percentage between samples of both Qena and Aswan increased more than 80%. Results of SDS-PAGE technique showed twelve protein bands (five monomorphic and seven polymorphic bands) and there aren't any protein bands found that might be reflected as a distinctive marker protein. It was also noted that both healthy and BBTV-infected samples from the same region were found together in a separate cluster.