The maintenance of stem cells within root meristem is the foundation for continuous growth of the root system. The PLETHORA (PLT) transcription factors have a function to control patterning of the root meristem, but the underlying molecular mechanism remains unclear. In this work we show that rice PLT3, PLT4 and PLT5 have a function to promote a repressive chromatin state to maintain stem cell fate in the root meristem. We show that PLT5 interacts with Polycomb Repressive Complex 2 (PRC2) that deposits the repressive mark H3K27me3 and the histone demethylase JMJ703 that removes the active mark H3K4me3 in rice root meristem cells. In addition, JMJ703 itself associates with PRC2 proteins. Loss of PLT3, PLT4 and PLT5 function resulted in decreased PRC2-association and H3K27me3, increased H3K4me3, and upregulated expression of genes decorated with the two marks in the root meristem. Further analysis indicates that the PLT interactions with PRC2 and JMJ703 enhance the H3K27me3/H3K4me3 ratio at a set of bivalent genes to maintain their silent state. These results uncover a chromatin mechanism by which PLTs control the stem cell fate in the rice root meristem.