Post-translational modifications of histones play an important chromatic role of a transcript activity in eukaryotes. Even though mRNA and long noncoding RNA (lncRNA) genes share similar biogenetic processes, these transcript classes may differ in many ways. However, knowledge about the crosstalk between histone methylations and the two types of sorghum genes is still ambiguous. In the present study, we reveal the genome-wide distribution of six histone modifications, namely, di- and trimethylation of H3K4 (H3K4me2 and H3K4me3), H3K27 (H3K27me2 and H3K27me3), and H3K36 (H3K36me2 and H3K36me3) in sorghum and analyze their functional relationships. Unlike other histone methylation, the codecoration of H3K4me3 and H3K36me3 is negatively associated with the production of lincRNAs in the context of active expression of mRNA genes. Our data demonstrated that H3K4me3 may act as a complementary component to H3K36me3 in the transcriptional regulatory process. Moreover, we observe that both H3K4me3 and H3K36me3 are involved in the negative-going regulation of plant lincRNA and mRNA genes. Our data provide a genome-wide landscape of histone methylation in sorghum, decrypt its reciprocity, and shed light on its transcriptional regulation roles in mRNA and lncRNA genes.