Epigenetic regulation involves modifications of chromatin components such as post-translational modifications of histone proteins, methylation of cytosines in deoxyribonucleic acid (DNA), the involvement of small RNA and chromatin remodeling. Numerous methods have been established to understand the epigenetic control of agronomically important traits. Chromatin immunoprecipitation with sequencing (ChIP-Seq) is widely used to identify the binding sites of transcription factors or modified histones on a genome-wide scale. Here, ChIP-Seq targeting H3K4me3 and H3K27me3 marks in oil palm spears were conducted to examine genomic regions enriched with these histone modifications. Due to low DNA amounts from ChIP experiments, the data analysis workflow was optimised based on ChIP-Seq workflows on other plants. Mapping to specific target regions revealed that the histone mark peak positions were located close to predicted transcription start sites (TSS). This agrees with H3K4me3 and H3K27me3 profiles in other plants where H3K4me3 marks are generally associated with active genes and promoter regions while H3K27me3 marks are linked to repressed genes. Gene-wide mapping for low coverage ChIP-Seq data showed that H3K4me3 and H3K27me3 profiles on the oil palm genome corresponded to consensus histone profiles in other plants. This is the first ChIP-Seq analysis workflow reported for oil palm spears, which can be used to develop future oil palm ChIP-Seq studies.