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Water shortage limits the production of fruit orchards, such as pear, in arid and semi-arid regions. The identification of wild pear germplasm for potential use as rootstock would be valuable for pear cultivation in semi-arid regions. The relative drought tolerance of wild pear germplasm (Pyrus boisseriana) from three different populations distributed along an elevational gradient ('semi-arid 1,000', 'semi-wet 1,350' and 'semi-wet 1,600' populations) was evaluated in a greenhouse trial. Established container-grown seedlings were exposed to 18 days of simulated drought, or not, followed by a seven day recovery period. Biomass allocation and accumulation, physiological (stomatal conductance, photosynthesis, transpiration, xylem water potential) and biochemical parameters (leaf pigments, free proline, malondialdehyde and hydrogen peroxide production) were evaluated. Although all populations were able to recover from water shortage, thereby proving to be relatively drought tolerant, some differences between populations were detected for gas exchange parameters, biomass accumulation and proline concentration in favor of the 'semi-arid 1,000' elevation population, which was more drought tolerant. This population showed the most rapid and complete recovery of physiological activity (stomatal conductance and carbon fixation). In addition, all populations showed an increase in carotenoid content in the leaves. Overall, we showed that plants from the 'semi-arid 1,000' elevation had greater tolerance to drought than those from the higher elevations (semi-wet populations). It therefore appears that plants from the 'semi-arid 1,000' elevation represent a promising source of material to be tested as rootstock for commercial scions of pear in field conditions in areas prone to suffer from water deficit.