The changes of rooting characteristics and contents of endogenous phenolic compounds were studied during the rooting period of cuttings of four elite Japanese larch (Larix kaempferi) clones, i.e., Rifu27-3-1, Rikuan 17-3-1, Ricao82-4-3, and Ricao103-3-1. Results showed that there were significant differences in the rooting characteristics of cuttings amongst different clones. Clones “Rifu27-3-1” and “Rikuan17-3-1” were easier to root than the other two clones. Marked differences were found in the variation of contents of endogenous phenolic compounds during the rooting period for the clones, but, in general, the total content of phenolic compounds decreased over the rooting period. The contents of phenolic compounds in two easy-to-root clones were lower than those of the two difficult to root. The contents of pyrocatechol, para hydroxyl-benzoic acid, ferulic acid, pyrocatechuic acid and gallic acid in clones “Rifu27-3-1” and “Rikuan17-3-1” decreased slightly during the rooting of cuttings, while the contents of pyrocatechol, ferulic acid, pyrocatechuic acid and gallic acid in clones “Ricao82-4-3” and “Ricao103-3-1” declined sharply with great fluctuation except for pyrocatechol which increased on the contrary. Generally, a significantly negative relationship existed between the contents of phenolic compounds and variables like rooting rate, number of roots and maximum root length. Restraining effects of phenolic compounds on rooting of cuttings varied.