||Post-translational modifications of histones are important chromatic players of transcriptional activity in eukaryotes. Even though mRNA and long noncoding RNA (lncRNA) genes share similar biogenetic processes, these transcript classes may differ in many regards. However, knowledge about the crosstalk between histone methylations and the two types of sorghum gene is still ambiguous. In the present study, we employed chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) to investigate 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 bicolor (L.) cultivar BTx623. These histone marks, excluding of H3K27me2, appear mainly in generic regions. With the exception of H3K36me2 which is evenly distributed within transcriptional regions, the rest of them are relatively enriched around the transcription start sites (TSSs) of mRNA genes. In addition, the absence of H3K4me3 and H3K36me3 is related to high tissue specificity of long intergenic noncoding RNAs (lincRNAs) in sorghum. Thus, we proposed that, unlike the other histone marks, these two marks may synergistically decrease the production of lincRNAs in the context of active expression of mRNA genes. H3K4me3 may act as a complementary to H3K36me3 in transcriptional regulatory process. Moreover, we observed that both H3K4me3 and H3K36me3 are involved in the regulation of plant mRNA and lincRNA genes. Our data provide a genome-wide landscape of histone methylation in sorghum, decrypt their reciprocity, and shed light on their transcriptional regulation roles in mRNA and lncRNA genes.