The effects of the removal of the shoot apex of tobacco on the relative transcript levels of potassium channel genes, determined by real-time PCR, and on the relationship between the expression of genes encoding potassium channels and potassium concentration, were studied. The results from the study indicated that comparatively more assimilates of photosynthesis were allocated to the apex in control plants than in both decapitated and IAA-treated decapitated plants. By contrast, dry matter in the upper leaves, roots, and stems in both decapitated and IAA-treated plants was significantly increased relative to control plants. The potassium level in whole plants decreased post-decapitation compared with control plants, and so did the potassium concentration in middle and upper leaves, stem, and roots. Expression of NKT1, NtKC1, NTORK1, and NKT2 was inhibited by decapitation in tobacco leaves with a gradual reduction after decapitation, but was induced in roots. The relative expression of NKT1, NTORK1, and NKT2 in tobacco leaves was higher than that in roots, whereas the expression of NtKC1 was higher in roots. The levels of inhibition and induction of NKT1, NtKC1, NTORK1, and NKT2 in leaves and roots, respectively, associated with decapitation were reduced by the application of IAA on the cut surface of the decapitated stem. Further results showed that the level of endogenous auxin IAA in decapitated plants, which dropped in leaves and increased in roots by 140.7% at 14 d compared with the control plant, might be attributed to the change in the expression of potassium channel genes. The results suggest that there is a reciprocal relationship among endogenous auxin IAA, expression of potassium channel genes and potassium accumulation. They further imply that the endogenous IAA probably plays a role in regulating the expression of potassium channel genes, and that variations in expression of these genes affected the accumulation and distribution of potassium in tobacco.