Optimal understanding of biodiversity threats must consider the effects of population size and habitat quality on population viability. I examined the effects and relative importance of these factors for the performance of two endangered hemiparasitic plants, Melampyrum cristatum and M. arvense in Finland. I surveyed 18 M. cristatum and 14 M. arvense populations. Both habitat quality and population size influenced the performance of M. cristatum. By contrast, the performance of M. arvense was determined by habitat quality, but not influenced by population size. Habitat quality was improved in managed M. cristatum populations, which translated into greater hemiparasite performance in these populations. Degradation of suitable habitats has likely decreased the performance of the two endangered hemiparasites, resulting in reduced population sizes. The results highlight the importance of considering simultaneously population size effects and habitat quality. Habitat management seems to be the key to sustain or increase the viability of the hemiparasite populations, but the timing and intensity of management should be considered.