Several benzoic and cinnamic acid derivatives were identified from cucumber root exudates. The effects of these phenylcarboxylic acids on root growth and cell cycle progression were examined in germinated seeds of cucumber. All 12 phenylcarboxylic acids (0.25 mM) tested significantly inhibited cucumber radicle growth, and cinnamic acid exerted a dose-dependent inhibitory effect. At 6 h after exposure to the acids, transcript levels of the cell cycle-related genes, including two cyclin-dependent kinases (CDKs) and four cyclins were reduced. Among them, transcript of CycB, a marker gene for mitosis showed a remarkable reduction. The temporal analysis showed that expression of mitotic genes (CDKB, CycA, and CycB) were reduced throughout the experiment, while the reduction of the other genes (CDKA, CycD3;1, and CycD3;2) were observed only at earlier time points. At 48 h after treatment with benzoic and cinnamic acids, an enhancement of endoreduplication was observed. Further time course analysis indicated that endoreduplication started as early as 6 h after exposure to cinnamic acid. These results provide evidence that exposure to benzoic and cinnamic acids can induce rapid and dramatic down-regulation of cell cycle-related genes, thus leading to root growth inhibition. Meanwhile, the block of mitosis caused by phenylcarboxylic acids also induced an increased level of endoreduplication.