Strong demand for palm oil creates a huge challenge for the industry to produce more palm oil on the shrinking cultivable land mass. Genetic manipulation of oil synthesis in the mesocarp tissue of oil palm offers the opportunity to improve yield and quality of palm oil on the limited land resources. However, more than one mesocarp-specific promoters are required to effectively manipulate oil synthesis to avoid epigenetic silencing caused by the sequence homology in their promoter regions. This study was aimed at identifying genes that are specifically expressed in the mesocarp tissue through in silico analysis of transcriptome datasets from different oil palm tissues. From this analysis, transcripts XLOC_10, annotated as pentatricopeptide repeat (PPR) protein was highly expressed in the mesocarp tissue. Gene expression analysis of PPR in 27 tissues of Elaeis guineensis indicated that this putative mesocarp-specific transcript was expressed in mesocarp and female inflorescence tissues only. Cis-acting elements that are present in the promoter region of PPR showed that PPR might be involved in the lipid biosynthesis and flowering regulation network in oil palm.