We examined the effects of size and spatial isolation of fens on the isozyme variability of 17 populations of Swertia perennis. This long-lived perennial is a locally abundant fen specialist in Switzerland, where wetlands have been strongly fragmented. Isozyme variability was comparable to other outcrossing plants (A = 1.53, AP_P = 2.01, P_P = 42.5, H₀ = 0.113, H₀ = 0.139). F statistics indicated both inbreeding within and differentiation between populations (F_IS = 0.076, F_IT = 0.194, F_ST= 0.128), with moderate gene llow between populations (N_em = 1.703). Populations in small, isolated fens had reduced genetic variability and the highest within-population inbreeding coefficients (F_IS). Isozyme variability was significantly associated with vegetative fitness traits (MANOVA), and the magnitude of leaf herbivory decreased as the percentage of polymorphic loci increased. These data suggest that the reduced genetic variability of S. perennis in small, isolated populations may reduce plant fitness, thereby increasing susceptibility to herbivore damage. Our study also shows that habitat fragmentation can reduce the genetic variability of populations of fairly common habitat specialists, which so far have attracted less conservation attention than rare species.