Banana streak virus (BSV) is a significant constraint to banana production in Kenya. The ability to quickly and reliably detect BSV is important for the management of the virus. Hence, detection of the variability of BSV was necessary for the optimization of a suitable diagnostic protocol to be used for routine screening of tissue cultured material. In this study, 215 potentially infected banana plants from nine major banana growing regions in Kenya were tested for BSV using serological and molecular techniques. Virus particles were detected by immunosorbent electron microscopy (ISEM) in seven of the ten tested samples confirming the presence of BSV. Immuno-capture-polymerase chain reaction (IC-PCR) using a degenerate primer was used on extracted viral DNA and on immune-captured viral particles from 80 samples. Enzyme-linked immunosorbent assay (ELISA) confirmed the presence of BSV in 200 samples and IC-PCR in 38 of the 80 tested samples. A total of 33 sequences were obtained from eight samples by PCR (EMBL accession numbers AM 905900-AM905905) across the conserved reverse transcriptase/RNaseH region of the genome. Pairwise comparison of the sequences suggested that they represented seven different isolates with sequence identity thresholds of 90-100%. Southern blotting and hybridization with a radiolabelled probe of the Lisulya clone, confirmed that both integrated and episomally replicating viral DNA may be present in at least one of the Kenya samples. Therefore, the presence of BSV in Kenya and some diversity within the Kenyan population was confirmed. The diagnostic protocol was optimized for the confirmed isolates.