In vitro rooting is very valuable for production of economically important plants. During the rooting process of cuttings in Taxus chinensis var. mairei, two types of rooted cuttings were examined, one type with a low rate of root formation and another type with a high rate of root formation. To determine the physiological role of indole-3-acetic acid (IAA), as well as free, conjugated, and bound polyamines (PAs) during the process of rooting, the amount of these compounds in the stem portion, needles, roots, and basal portion of cuttings were measured. Compared to the cuttings with low rate of root formation, cuttings with high rate of root formation had higher concentration of IAA in the stem portion and basal portion of the rooted cuttings 7 weeks after planting. An increase in IAA contents was also observed in tips of roots and lateral roots of cuttings. The content of free putrescine (Put) was increased and the content of conjugated Put was decreased in the basal portion and stem portion, but not in the needles of cuttings during planting. The content of free spermidine (Spd) was decreased in the basal portion, needle, and stem portion of cuttings. The conjugated Spd was decreased in the basal portion of cuttings. In the cuttings of T. chinensis var. mairei, the content of free spermine (Spm) was not change in the basal portion, needle, and stem portion, but the content of conjugated Spm was decreased in the stem portion and the content of bound Spm was decreased in needles and stem portion of cuttings 9 weeks after planting. Changes of these endogenous factors are associated with the rooting features of T. chinensis var. mairei cuttings and their functions have been discussed.