Outbreaks of whitefly,Bemisia tabacispecies in East and Central Africa, have become increasingly prevalent during the previous 25 years and are responsible for driving the spread of plant-virus diseases, such as cassava mosaic disease and cassava brown steak disease. Epidemics of these diseases have expanded their ranges over the same period, spreading from Uganda into other sub-Saharan African countries. It was hypothesised that a highly abundant ‘invader’ population ofB.tabaciwas responsible for spreading these diseases from Uganda to neighbouring countries and potentially hybridising with the resident cassavaB.tabacipopulations. Here, we test this hypothesis by investigating the molecular identities of the highly abundant cassavaB.tabacipopulations from their supposed origin in Uganda, to the northern, central, eastern and coastal regions of Tanzania. Partial mitochondrial cytochrome oxidase I (mtCOI) barcoding sequences and nuclear microsatellite markers were used to analyse the population genetic diversity and structure of 2734B.tabacicollected from both countries and in different agroecological zones. The results revealed that: (i) the putative SSA1 species is structured according to countries, so differ between them. (ii) Restricted gene flow occurred between SSA1–SG3 and both other SSA1 subgroups (SG1 and SG2), even in sympatry, demonstrating strong barriers to hybridization between those genotypes. (iii) Not onlyB.tabaciSSA1-(SG1 and SG2) was found in highly abundant (outbreak) numbers, butB.tabaciSSA1-SG3 and the Indian Ocean (IO) species were also recorded in high numbers in several sites in Tanzania. (iv) The SSA1-(SG1 and SG2) species was distributed in both countries, but in Tanzania, theB.tabaciIO and SSA1–SG3 species predominated. These data confirm that multiple, local TanzanianB.tabacispecies produce highly abundant populations, independent of the spread of the putative invasiveB.tabaciSSA1-(SG1 and SG2) populations.