Morpho-physiological characteristics in Eucalyptus species can determine N (NUE) and P (PUE) use efficiency and, consequently, the plant's responses to fertilization. The study aimed to evaluate whether morphological and physiological characteristics of seedlings from Eucalyptus species affect the N and P use efficiency. For this, in a greenhouse, Eucalyptus grandis (GPC 23) and Eucalyptus saligna (32864) clones were grown in Hoagland nutrient solution for 21 days, followed by N and P restriction in CaSO4 solution 0.1 mol L-1 during 15 days. Morphological parameters from shoot and root system, dry mass of organs, photosynthetic pigments concentration, and chlorophyll a fluorescence of Eucalyptus species were evaluated, and NUE and PUE were calculated. Eucalyptus grandis presented the highest NUE and PUE values. The highest surface area, volume, and roots length values contributed to these results, justifying the highest dry mass production from leaves, stem, roots, and plant. Eucalyptus saligna presented the lowest NUE and PUE values, which negatively influenced photosynthesis (higher F-0 values and lower concentrations of photosynthetic pigments). Root morphological parameters had a strong relationship with NUE and PUE and can be used to select Eucalyptus species, and breeding programs, as they can predict the ability of development of Eucalyptus species under low N and P availability.