This study was conducted to examine the water use efficiency (WUE) in five species of one-year-old seedlings grown in a field nursery in Mongolia. Larix sibirica and Pinus sylvestris are the most dominant coniferous species while Ulmus pumila is an important deciduous species known well-adapted in harsh conditions such as in semi-arid forests and Gobi desert regions. Caragana arborescens (Siberian pea shrub) and Hippophae rhamnoides are N-fixing shrubs in Mongolia. Thirty one-year-old seedlings were sampled from each of the five species (a total of 150 samples) and measured for net photosynthetic rate (Pn) and transpiration rate (E). The Pn and E were used to calculate and compare the WUE of each species. Pn differed significantly among the five species (p < 0.05). However, there was no significant difference in Pn between L. sibirica and H. rhamnoides (p > 0.05). C. arborescens showed the highest Pn whereas U. pumila did the poorest. E differed significantly among the five species (p < 0.05). L. sibirica and U. pumila showed considerably lower E than other species. Thus, WUE values of coniferous species such as L. sibirica and P. sylvestris were significantly greater than deciduous or shrub species such as U. pumila, C. arborescens and H. rhamnoides (p < 0.01). It may result that conifers showed relatively high water use efficiency than deciduous or shrub trees due to their lower transpiration rates, which resulted in morphological and physiological characteristics of their leaves. This may indicate that L. sibirica and P. sylvestris can be widely used for rehabilitation works in Mongolia attributed to their dominant distributions but also their high drought-resistance properties.