The dynamics of resistance in the sweetpotato whitefly, Bemisia tabaci (Gennadius), to the neonicotinoids acetamiprid and thiamethoxam was studied extensively in cotton fields in Israel during the cotton-growing seasons 1999–2003. Whitefly strains were collected in early and late seasons mainly in three locations in northern, central, and southern Israel. The whiteflies were assayed under laboratory conditions for susceptibility to neonicotinoids, as part of the Israeli cotton insecticide resistance management strategy. Selections to both acetamiprid and thiamethoxam and cross-resistance between them also were conducted in the laboratory. Although no appreciable resistance to acetamiprid was observed up to 2001, a slight increase of approximately five-fold resistance was detected during 2002 and 2003. However, from 2001 to 2003 thiamethoxam resistance increased >100-fold in the Ayalon Valley and Carmel Coast cotton fields. In cross-resistance assays with both neonicotinoids, the strain that had been selected with thiamethoxam for 12 generations demonstrated almost no cross-resistance to acetamiprid, whereas the acetamiprid-selected strain exhibited high cross-resistance of >500-fold to thiamethoxam.