We studied effects of inbreeding on the early fitness measures seed production and germination in Swertia perennis L. (Gentianaceae), a locally abundant specialist of fen grasslands, which have been greatly fragmented in Switzerland. We further tested whether such effects differed between populations of different size and isolation. We studied effects of free pollination, hand-outcrossing and hand-selfing on 160 plants in 16 populations in large, in small barely isolated, and in small isolated habitat islands. We found a distinct gradient in experimental outcomes from free pollination to hand-outcrossing to hand-selfing. Compared with free pollination, selfing reduced the number of seeds per capsule by 22% (P < 0.01), the seed/ovule ratio by 26% (P < 0.001), seed mass by 25% (P < 0.001) and germination percentage by 23% (P < 0.05). The outcome of hand-outcrossing was intermediate for all traits. The reduction in early fitness components after selfing is most likely due to inbreeding depression. Higher seed production and germination after free pollination than after hand-outcrossing may be due to a larger number of pollen donors involved in free pollination or due to higher quality of free pollen because of lower relatedness of parent plants. Moreover, the fact that seed production was highest after free pollination indicates that S. perennis is not pollen limited. Pollination treatment effects did not differ between different island types. Hence, there are no indications that early inbreeding depression was purged from more strongly fragmented populations.