Bemisia tabaci populations belonging to Middle East-Asia Minor one (MEAM1) and Mediterranean (MED) groups (formerly biotype B and Q, respectively) have spread throughout the world. Although the introduction of MEAM1 is documented from several Caribbean islands, it is generally not known whether MED has also been introduced; whether indigenous populations have survived; and if in the affirmative, to which group(s) they belonged. Whiteflies were collected from seven islands on various plant species. The prevalence of MEAM1 and non-MEAM1 individuals was assessed using a microsatellite approach validated with sequences of the mitochondrial cytochrome oxidase I (mtCOI) gene. Of the 262 samples tested, 247 exhibited the MEAM1 pattern, whereas none showed the MED pattern. The mtCOI gene was partially sequenced from a sample of individuals exhibiting MEAM1 (n = 15) and non-MEAM1 patterns (n = 8) and compared with type sequences. The 15 individuals exhibiting the MEAM1 pattern were confirmed to belong to MEAM1. Of the eight individuals representative of the six non-MEAM1 patterns, two belonged to the indigenous New World (NW) group of B. tabaci (NW), one belonged to a distinct species of Bemisia, and five belonged to MEAM1. One individual belonging to NW exhibited 99.9% nucleotide identity with a NW individual from Puerto Rico. The other was identified as the most divergent individual of the North and Central American genetic cluster. We conclude that a highly homogenous MEAM1 population has extensively settled in the Caribbean and that heterogeneous NW populations were still detectable although severely displaced.