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Abstract: This study reports the characterization of Hop stunt viroid which has been isolated previously in Egypt from sweet orange infected with gummy bark disease namely citrus viroid II. The native structure of mature, circular forms of the gummy bark agent was detected by gel electrophoresis. The expected size of amplified cDNA by RT-PCR was approximately 300 bp. A phylogenetic tree of the Egyptian citrus gummy bark agent (Accession no. FJ984562) revealed 100, 99.7 and 97.8% a moderate degree of similarity to CVd-IIb (USA), CCaVd (Spain) and CCaVd (Egypt), respectively. The minimum free energy of a secondary structure for HSVd-EG-RNA was determined using its primary sequence at 37°C. The sequence appeared to fold into a rod-like structure at -122.1 kcal moL-1 while CCaVd-EG at -120.5 kcal moL-1. The five domains of the rod-like structure were determined. The sequence variations between Egyptian citrus gummy bark isolate and Egyptian citrus cachexia isolate in the pathogenic domain (P) tend to influence the pathogenicity of the HSVd-EG. Finally, the genetic diversity and evaluation of entropy power for the Egyptian citrus gummy bark agent and HSVd-citrus populations registered in GenBank, were viewed against the phylogenetic background of known CVd-II variants including the non-cachexia (CVd-IIa) and the causal agents of severe (CVd-IIb, CVd-IIc), more moderate (Ca903) and mild (Ca909).