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How climate-change induced environmental stress may alter the effects of inbreeding in patchy populations of rare species is poorly understood. We investigated the fitness of progeny from experimental self-and cross-pollinations in eight populations of different size of Echium wildpretii, a rare endemic plant of the arid subalpine zone of the Canarian island of Tenerife. As control treatments we used open pollination and autonomous selfing. The seed set of open-pollinated flowers was 55% higher than that of autonomously selfed flowers, showing the importance of animal pollination for reproductive success. The seed set, seed mass and germination rate of seedlings of hand-selfed flowers was similar to that of hand-crossed flowers, indicating weak inbreeding depression (seed set -4.4%, seed mass -4.1%, germination -7.3%). Similarly, under normal watering there were no significant effects of inbreeding on seedling survival (-3.0%). However, under low watering of seedlings inbreeding depression was high (survival -50.2%). Seed set of open- and hand-outcrossed-pollinated flowers was higher in large than in small populations, possibly due to more frequent biparental inbreeding in the latter. However, later measures of progeny fitness were not significantly influenced by population size. We predict that increasing drought duration and frequency due to climate change and reductions of population sizes may increase inbreeding depression in this charismatic plant species and thus threaten its future survival in the longer term.