In much of Western Europe, orchid species have suffered dramatic declines in abundance, whereas the remaining populations often tend to be small and isolated, occur in ecologically marginal habitats and may show decreased reproductive output due to altered pollinator interactions or the absence of specialized pollinators. Furthermore, small and isolated populations are expected to suffer from genetic erosion and increasing genetic divergence among populations, through the effects of random genetic drift, increased levels of inbreeding and reduced gene flow, potentially leading to reduced possibilities of population recovery in the future. In this study, genetic diversity and fitness variation were studied in nine fragmented populations of the food deceptive orchid Orchis purpurea. Within-population genetic diversity and among-population differentiation were investigated using dominant AFLP markers. All studied populations were relatively small (range 12-302; mean: 90 individuals/population). Despite their small size, genetic diversity within populations was rather high (mean gene diversity H-j: 0.21, range: 0.15-0.27) and genetic differentiation among populations was not higher than that typically observed in deceptive orchids (F-ST = 0.09). Nevertheless, Mantel tests showed a positive correlation between geographical and genetic distances indicating limited gene flow among populations. Fruit set, on the other hand, was very low (average fruit set: 5.5%), suggesting strong pollinator limitation, which, in turn, resulted in very low recruitment rates (average seedling recruitment per flowering individual: 0.12). Both measures significantly increased with increasing population size, indicating that a certain threshold value (> 50 flowering individuals) has to be reached to produce a sizeable number of fruits and seedlings. These results suggest that although deceptive pollination clearly results in a fitness cost, it may serve as an effective means to maintain high gene diversity within and to counter high genetic differentiation among small orchid populations. From a genetic point of view, our results further suggest that small populations of orchid species, should not be neglected as they may harbour as much genetic diversity as large populations. (c) 2007 Elsevier Ltd. All rights reserved.