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Limited data are available on the physiological responses of <i>Citrus</i> to nitrogen (N) deficiency. ‘Xuegan’ (<i>Citrus sinensis</i> (L.) Osbeck) and ‘Shantian pummelo’ (<i>Citrus grandis</i> (L.) Osbeck) seedlings were fertilized with nutrient solution at a N concentration of 0, 5, 10, 15 or 20 mM for 10 weeks. N deficiency decreased N uptake and N concentration in leaves, stems and roots and disturbed nutrient balance and homeostasis in plants, thus inhibiting plant growth, as well as reducing photosynthetic pigment levels and impairing thylakoid structure and photosynthetic electron transport chain (PETC) in leaves, hence lowering CO₂ assimilation. The imbalance of nutrients intensified N deficiency’s adverse impacts on biomass, PETC, CO₂ assimilation and biosynthesis of photosynthetic pigments. <i>Citrus</i> displayed adaptive responses to N deficiency, including (a) elevating the distributions of N and other elements in roots, as well as root dry weight (DW)/shoot DW ratio and root-surface-per-unit volume and (b) improving photosynthetic N use efficiency (PNUE). In general, N deficiency had less impact on biomass and photosynthetic pigment levels in <i>C. grandis</i> than in <i>C. sinensis</i> seedlings, demonstrating that the tolerance of <i>C. grandis</i> seedlings to N deficiency was slightly higher than that of <i>C. sinensis</i> seedlings, which might be related to the higher PNUE of the former.