Oxalis pes–caprae, a native of South Africa is a very successful, globally widely distributed, aggressive colonizer weed. It spreads vegetatively (through bulbils and underground shoots) in most of its colonized areas. In Israel, it is characterized by the total lack of seed set. Using 121 amplified fragment length polymorphism (AFLP) putative loci we have analysed the genetic structure of five representative populations in Israel. Despite the complete lack of sexual reproduction and the total dependency on vegetative dispersal, populations were found to be genetically variable. Surprisingly, considerable genetic diversity was found within and between all of the populations tested. We speculate that this diversity could be the result of an accumulation of mutations or genome rearrangement.