The genetic diversity within and among populations of Xanthoria parietina was studied at the subspecific level with a fingerprinting technique (RAPD-PCR) applied to sterile cultured multispore isolates, each being derived from a single apothecium. Populations from coastal, rural and urban sites from NW, SW and central France and from NE Switzerland were investigated. Between 1 and 8 microsites of a few decimetres square, each comprising 13 to 27 thalli of X. parietina, were analysed per population. A total of 132 isolates from epiphytic and 3 isolates from epilithic specimens were investigated. Phenotypic variation was recorded among some of the thalli in the field and among sterile cultured isolates in the laboratory. A high diversity of genotypes was observed, even among thalli growing side by side in phenotypically homogenous populations. An average of 73·5 % polymorphism was found in all samples. As shown with Principal Coordinates Analysis (PCO), most of the genetic variation (90%) resided within, not among, populations. As X. parietina had previously been shown with molecular and fingerprinting techniques to be homothallic, the potential genetic background of this diversity is discussed. Intense genotype rather than gene (allele) flow seems to be an important element in X. parietina populations.