Abstract: Background and Objective: Badnaviruses are serious plant pararetroviruses affecting several economic plants resulting in heavy losses worldwide. No previous studies were available on the phenomenon of chlorotic spot in Bougainvillea in Egypt. This study aims to elucidate the virus nature infecting B. glabra in Egypt. Materials and Methods: Immunocapture PCR (IC-PCR) used local antiserum for Banana Streak Virus (BSV) and the Badna FP/RP specific primers for the RT and RNase H coding regions of ORF3 present in badnaviruses. Amplified DNAs were inserted into pTZ57R/T vector and cloned in Escherichia coli JM 109 cells. Obtained sequence was blasted with other badnaviruses using BLASTN programs. Genetic Distance (GD) and phylogenic studies for this virus and other described badnaviruses were analyzed with MEGA6 program. Results: The IC-PCR yielded 580 bp amplicons from B. glabra, banana and sugarcane infected with BSV and Sugarcane Bacilliform Virus (SCBV), respectively. Accession # KM821771.1 was assigned for the new badnavirus from B. glabra. The virus had a maximum nucleotide identity of 75% and GD>0.2 with three Bougainvillea infecting viruses from Taiwan, Brazil and India, respectively. In phylogenetic analysis, it clustered with badnaviruses infecting B. spectabilis. These data indicate that chlorotic spots associated with B. glabra in Egypt are caused by a new Badnavirus species. A tentative name of Bougainvillea glabra Chlorotic Spot Virus-Egypt (BgCSV-E) was suggested. Conclusion: Serologic, molecular and phylogenetic tools unveiled the viral nature of the badnavirus causing chlorotic spot in Bougainvillea glabra plants in Egypt. The spread of BgCSV-E over neighboring areas may be possible and could represent a potential reservoir of the virus for other susceptible crops.