Bemisia tabaci is a species of sap-sucking insect belonging to the Aleyrodidae and are commonly known as whiteflies. The species is made up of a complex of distinct genetic groups which have a strong geographic pattern to their genetic structure. Two members of this complex known as the B and Q biotypes have proven to be particularly invasive, spreading with the aid of trade in ornamental plants, well beyond their home ranges across the Mediterranean Basin, Middle East and Asia Minor. This study uses DNA microsatellites to identify another biological invasion this time involving a B. tabaci from south east Asia. We provide evidence which supports an invasion sometime between 1994 and 1999 of B. tabaci from central Thailand into the Indonesian islands of Sumatra then Java and Bali. The invasion is also associated with the invasion of pepper yellow leaf curl virus, a begomovirus transmitted by B. tabaci, which is also shown to have a probable origin in the same geographic region as the invading whitefly. The consequences of the invasion of a plant-infecting virus and its vector has been a massive increase in the scale and impact of begomoviruses in tomato and chilli production which has seen regional bans imposed on the planting of chilli, an important cash crop for many village farmers in Sumatra and Java.