Banana streak viruses (BSVs) infect banana worldwide. BSV sequences present in the genome of Musa balbisiana hamper the detection of cognate episomal viruses by PCR, since PCR results in the amplification of both episomal viral DNA and integrated viral sequences, leading to false positives. A simple single-step multiplex immunocapture PCR (M-IC-PCR) assay was developed for the detection of only episomal BSV. This technique was applied in a study of the occurrence of BSV in Guadeloupe. Leaf samples from the main banana genotypes were indexed for the presence of major BSV species. Although no symptoms could be observed, BSV was found to be common in plantain (AAB), probably as a result of the widespread use of contaminated suckers. In contrast, BSV was uncommon on dessert banana cultivars (AAA), showing that the use of virus-free certified in vitro plants is an efficient strategy for controlling the spread of BSV, and that vector-borne transmission of BSV from plantain to dessert banana is very low in Guadeloupe. Our study also showed that Banana streak GF virus is the most prevalent species in Guadeloupe, with species Banana streak OL virus and Banana streak Mysore virus present at much lower levels. Using the same leaf samples, a study on the occurrence and diversity of Banana virus X (BVX), a member of the Flexiviridae family, which has been recently described and characterised in Guadeloupe, was undertaken. Indexing by direct-binding reverse transcription PCR showed that BVX is very uncommon in Guadeloupe and has a low level of molecular diversity. This is in contrast to Banana mild mosaic virus, which is a closely related member of the Flexiviridae family, and for which an immunocapture reverse transcription nested PCR detection method was established.