Banana bunchy top virus (BBTV, genus Babuvirus, family Nanoviridae) is the most damaging viral agent of bananas and plantains. BBTV is a multipartite virus composed of 6 circular single-stranded DNA components. BBTV is sometimes associated with an additional component named alphasatellite. Alphasatellites are not essential for infection and need a helper virus for movement, encapsidation and plant-to-plant transmission. The role of alphasatellites has been poorly studied, especially for BBTV associated alphasatellites. Our de novo reconstruction of BBTV from viruliferous banana aphids in Democratic Republic of Congo (DRC) by rolling circle amplification of viral DNA, followed by Illumina sequencing and bioinformatics, revealed the presence of a novel alphasatellite in addition to six core components of the viral genome. This is the first alphasatellite identified in the "South Pacific" phylogenetic group of BBTV isolates. Phylogenetic analysis using pairwise and multiple alignment revealed that DRC-alphasatellite belongs to the subfamily Nanoalphasatellitinae of the family Alphasatellitidae and represents the first member of a new alphasatellite genus. Immunocapture-PCR diagnostics and cloning strategies, designed based on the de novo reconstructed sequences of BBTV-DRC components including DNA-alpha, validated the Illumina sequencing results, and demonstrated that DRC-alphasatellite was encapsidated with the BBTV coat protein. Blot hybridization analysis of virus-derived small interfering RNAs (siRNAs) in BBTV-infected banana plants revealed that DRC alphasatellite alters production of siRNAs from the core components of BBTV genome, suggesting its interaction with the plant antiviral defense based on RNA interference and gene silencing. Taken together our findings shed a new light on mysteries surrounding alphasatellites and invite for further investigation into the role of alphasatellites in banana bunchy top disease.