Abstract: This study investigated the relationship between the development of tomato lateral roots and auxin, NAC1 (transcription factor involved in the auxin signal transduction) and miR164 expression under P deficiency. Effects of exogenous auxin NAA (1-naphthalene acetic acid) and its transport inhibitor NPA (N-1-naphthylphthalamic acid) on the lateral root development were analyzed under P deficiency (5 μmol/L Pi) versus the control (500 μmol/L Pi). The time course of the expression pattern of miR164 and its target gene, NAC1, were analyzed by RT-PCR. The results showed that the development of lateral roots was promoted by NAA and blocked by NPA. During 12 h of lateral root initiation, expression of NAC1 was strongly up-regulated, while miR164 was down-regulated in P-deficient plants. Our data suggest that miR164, together with its target (NAC1), is involved in the mediation of P-deficiency-induced lateral root development.