More efficient photosynthesis has allowed C₄ plants to adapt to more diverse ecosystems (such as hot and arid conditions) than C₃ plants. To better understand C₄ photosynthesis, we investigated the expression patterns of C₄ genes (C4PPDK and PCK1) and their non-C₄homologous genes (CyPPDK1, CyPPDK2, and PCK2) in the different organs of maize (Zea mays). Both C₄ genes and non-C₄ genes showed organ-dependent expression patterns. The mRNA levels of C₄ genes were more abundant in leaf organ than in seeds at 25 days after pollination (DAP), while non-C₄ genes were mainly expressed in developing seeds. Further, acetylation of histone H3 lysine 9 (H3K9ac) positively correlates with mRNA levels of C₄ genes (C4PPDK and PCK1) in roots, stems, leaves, and seeds at 25 DAP, acetylation of histone H4 lysine 5 (H4K5ac) in the promoter regions of both C₄ (C4PPDK and PCK1) and non-C₄ genes (CyPPDK1, CyPPDK2, and PCK2) correlated well with their transcripts abundance in stems. In photosynthetic organs (stems and leaves), dimethylation of histone H3 lysine 9 (H3K9me2) negatively correlated with mRNA levels of both C₄ and non-C₄ genes. Taken together, our data suggest that histone modification was involved in the transcription regulation of both C₄ genes and non-C₄ genes, which might provide a clue of the functional evolution of C₄ genes.