23The Bemisia cassava whitefly complex includes species that cause severe crop damage 24 through vectoring cassava viruses in eastern Africa. Currently, the cassava whitefly complex 25 is divided into species and subgroups based on very limited molecular markers that did not 26 allow clear definition of species and population structure. Based on 14,358 genome-wide 27 SNPs from 63 cassava whitefly individuals belonging to sub-Saharan African (SSA1, SSA2 28 and SSA4) species, and using a well-curated mtCOI gene database, we show clear 29 incongruities in previous taxonomic approaches underpinned by effects from pseudogenes. 30We show that the SSA4 species is part of the SSA2 species, and that populations of the SSA1 31 species comprise of south-eastern (Madagascar, Tanzania) and north-western (Nigeria, 32 Democratic Republic of Congo and Burundi) sub-species that show signatures of allopatric 33 incipient speciation, with a hybrid zone separating these adjacent sub-species. These findings 34 provide the first genomic insights into the evolution and molecular ecology of a highly 35 cryptic hemipteran insect complex in African, and allow the systematic use of genomic data 36 in management and control strategies for this important cassava pest. 37 38