<p>Banana bunchy top virus (BBTV) is a major threat to banana and plantain cultivation in several tropical and sub-tropical regions of the world including India, causing significant yield losses. Despite removal of symptomatic bunchy top infected plants and chemical control of aphids in the field, the disease is not completely eliminated. To investigate the latency phenomenon associated with banana bunchy top disease, experiments were conducted. In the transmission assay for BBTV in cv. Grand Nain (AAA) with the viruliferous banana black aphid (<i>Pentalonia nigronervosa</i>), 56.56% of plants expressed typical symptoms within 35 days after inoculation (DAI) whereas 29.1% showed symptoms between 36 and 70 DAI. Interestingly, 1.64% of plants remain asymptomatic upto 257.93 days. Upon quantification of viral titre during the latent period through SYBR green-based qPCR assay, virus copy number was found to be negatively correlated with latency duration. Furthermore, plants with a disease scale of 5 showed a maximum transmission rate of 60%, whereas asymptomatic banana plants (cv. Grand Nain) still showed a transmission rate of 3–6%. These results show the existence of BBTV in a latent form in asymptomatic banana plants and emphasize the importance of creating awareness among the tissue culture industries and farmers about virus indexing and the use of virus-free planting materials. This study is the first of its kind to expatiate upon the latency exhibited by BBTV in banana.</p>