Alligator weed, Alternanthera philoxeroides (Mart.) Griseb., is one of the worst invasive weeds in theworld. In the present study, the genome size of seven forms/biotypes of alligator weed from Argentina (native area),the USA (introduced area), and China (introduced area) was analyzed using flow cytometers; the ribosomalDNA internal transcribed spacer region (ITS) was cloned and sequenced. We found that the genome size ofA. philoxeroides ranged from 5.72 to 8.50 pg/2C nucleus, consisting of four levels of genome and three kinds of ploidy.Among them, three levels and two kinds (tetraploid and hexaploid) were found in samples from Argentina, two levelsand one kind (pentaploid) in US samples, and one level and one kind (hexaploid) in samples from China. Contrary tothe signi ficant variation in genome size, we found that the intraspeci fic differentiation of the ITS sequences in theseven forms/biotypes was extremely low, and that six of them shared ITS sequences with no or one singlesubstitution. These results show that the change of genome size played a major role in the differentiation ofA. philoxeroides, and that forms/biotypes with higher ploidy seem to have stronger invasive ability. Furthermore, thedifferences of A. philoxeroides in ploidy between samples from the USA and China showed that alligator weeds fromthese two invaded areas certainly have different native progenitors