Stem cell maintenance and differentiation are regulated by histone modifications both in cytoplasm and nucleus; however, little is known about the dynamic profiles of histone modifications on a cellular level during flowering transition and floral organ differentiation in plants. Here, the dynamic profiles of histone modifications in the SAM and inflorescence of Rice (Oryza sativa L. ssp. Japonica) were investigated using immunofluorescence analysis. The cytoplasmic monomethylated at histone lysine 9 (H3K9me1) and acetylation on histone H3 (H3ace) were observed during floral organ differentiation. In addition, our results indicated that the levels and profiles of histone modifications might be associated with the plant's stem cell division and differentiation. Thus we concluded that vegetative growth and floral organ differentiation could be regulated by global histone modifications in a cell-specific fashion via modification in both nucleus and cytoplasm.