The onion thrips, Thrips tabaci (Lindeman), is the only known vector of Iris yellow spot virus (IYSV). IYSV was detected in Georgia for the first time in 2003. Phylogenetic analysis using nucleotide sequences of the IYSV capsid gene indicated that it may have been accidentally introduced from repackaging of imported Peruvian onions in the Vidalia onion-growing region. The tobacco thrips, Frankliniella fusca (Hinds), has been the dominant thrips species on onions in Georgia. However, in recent years the incidence of T. tabaci on onions has been consistently increasing. Laboratory competition studies indicated that T. tabaci outcompeted F. fusca on onion foliage. This led to speculation that a new biotype of T. tabaci may have been introduced along with IYSV through importation of Peruvian onions. This hypothesis was tested by analyzing variations in the mitochondrial cytochrome oxidase I gene and internal transcribed spacer region 2 of T. tabaci populations from Georgia and Peru. DNA was extracted from T. tabaci samples from Georgia and Peru and subjected to PCR using specific primers. The resulting amplicons were sequenced. Parsimony and Bayesian analysis of the COI sequences indicated that all the Peruvian taxa fell into a single clade along with one Georgia taxon. All the other Georgia taxa were in a separate clade. ITS2 sequence comparisons indicated that Georgia and Peru taxa were found in numerous clades. High variation among taxa from each region indicated that ITS2 may not be suitable to assess intraspecific variation among T. tabaci populations.