In order to make a rough drawing of H3K9ac and identify genes which regulated by H3K9ac modification, provide information for regulation of gene expression in Hippophae rhamnoides, western blot and ChIPseq were carried out. The results showed that the binding capacity of H3K9ac antibody with histone of H. rhamnoides is tightness. Highthroughput sequencing of enrichmental DNA fragments obtained 2.2×10⁷ and 3.6×10⁷ raw reads. Unique mapped reads were widely distributed in the genome of H. rhamnoides and obviously enriched in both ends of the structural genes. There are 1 011 peaks were identified by predicting the functions of gene enrichment areas, these results showed that H3K9ac played important roles in gene expression of H. rhamnoides. The enrichment and highthroughput sequencing of DNA fragments of H. rhamnoides proves that antibodies can be used to study the types of histone modification. The first H3K9ac modification sketches of genetic and the genes regulated by H3K9ac were identified. It is important for investigating genes expression of H. rhamnoides regulated by histone modification.