Phosphate (Pi) transporters in plant roots play a major role in phosphate uptake from the soil. The Pht1 family genes are the most important Pi transporter genes and their expression is usually induced under phosphorus (P) deficient conditions. So far it is unclear how eucalypts are able to grow well in P-deficient conditions. The objective of this study was to investigate Pht1 gene family and their expression in eucalypts under different P levels. Two eucalypt species, Eucalyptus dunnii and Corymbia citriodora were grown hydroponically at six P levels (0, 0.01, 0.1, 0.5, 1 and 2 mM). Lower P levels (i.e. 0 and 0.01 mM P) and the highest P concentration (2.0 mM) reduced seedling growth for both E. dunnii and C. citriodora. Members of the Pht1 gene family were identified in C. citriodora (CcPt1 and CcPt2) and in E. dunnii (EdPt1 and EdPt2). The expression of the Pht1 family genes was negatively correlated with the P level applied. At 0 mM and 0.01 mM P supply level, CcPt1, CcPt2 and EdPt1 were up-regulated, but no up-regulation of expression was detectable at higher P supply levels, indicating a P deficiency-induced Pht1 family gene expression. The expression of the Pht1 family genes were higher in E. dunnii than in C. citriodora, suggesting higher P demand of the former than the latter, which matches the higher growth rate of E. dunnii than that of C. citriodora seedlings. The expression of the putative phosphate transporter genes increased with seedling age for E. dunnii but not for C. citriodora, implying that C. citriodora is less sensitive to P deficiency. The present study contributes to a better understanding of the physiological mechanisms for survival and growth of eucalyptus in P deficient environments, and provides basic knowledge for silviculture and management of eucalypts plantations.