AFLP analysis was used to evaluate the genetic variation of the mangosteen (~iGarcinia mangostana~i L), which is an asexual and agamosperous fruit tree. Twenty-three samples of ~iG. mangostana~i were collected from Thailand, Indonesia and Malaysia.In addition, two related species of ~iG. mangostana, G. hombroniana~i Pierre and~iG. malaccensis~i Hook, were used to evaluate the variation within species. A total of 477scorable bands were obtained using 10 primer pairs in 23 plants of ~iG. mangastana~i and41 polymorphic bands were detected from 9 primer pairs. It is remarkable that intraspecific variations exist in ~iG. mangostana~i, although the level of polymorphismswas relatively low when compared to the two related species. Since ~iG. mangostana~i isagamospermy and always produces seeds without fertilization, it seems likely that all mangosteen trees are somatic clone. The genetic variations among ~iG. mangostana~i areprobably due to the somatic mutation while the variations in G. malaccensis and~iG. hombroniana~i, which are considered to be facultative agamosperms, are due to sexualreproduction. We concluded that AFLP analysis is a useful tool to detect genetic variation of mangosteen. The phylogenetic relationships among 17 Garcinia species including ~iG. manostana~i (mangosteen) were analyzed by comparing sequences of theinternal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA). Both parsimonious and neighbor joining (Nn analyses revealed that ~iG. mangostana~i is closelyrelated to ~iG. malaccensis~i said to be a progenitor of mangosteen. Although anothersuspected progenitor of mangsteen, ~iG. hombroniarur~i, was more far distant from G.mangostana than ~iG. malaccensis~i phylogenetically. Garcinia hombronianaformed a cluster with ~iG. rostrata, G. speciosa~i and ~iG. sirygifolia~i, and this clusterwas connected with a cluster of ~iG. mangostana~i and ~iG. malaccensis~i. The ITS sequenceanalysis showed that ~iG. atrovfridis, G. cowa, G. dulcis, G. malaccensis. G.mangostana, G. rostratd and G. vilersiarra~i have nucleotide additivity (two differentnucleotides at the same locus) at several sites in the ITS region. The occurrence of these species might be related to hybridization with ancestors, but the genomic compositions, even chromosome numbers, of these species are still unknown.