Begomoviruses are transmitted by whiteflies in a persistent manner, but factors responsible for the variation of virus transmission by different species are poorly understood. We examined ingestion of papaya leaf curl China virus (PaLCuCNV) and tomato yellow leaf curl virus (TYLCV) by two species of the Bemisia tabaci complex, MEAM1 and MED, and then quantified the virion concentrations in different organs/tissues in each species. We found that PaLCuCNV penetrated the midgut wall of MED less efficiently than MEAM1, resulting in lower efficiency of PalCuCNV transmission by MED than that by MEAM1, while TYLCV penetrated the midgut wall of both species and was transmitted by them at similar levels of efficiency. Virus coat protein determined the virus capacity to cross the midgut wall of a given whitefly species. These data indicate that the level of midgut penetration determines virus acquisition and transmission by whiteflies in the first instance.