Arabidopsis WRINKLED1 (AtWRI1) (At3g54320) is a pivotal transcription factor in the regulation of plant oil biosynthesis. Our previous study identified a WRI1 homolog highly expressed in oil palm mesocarp (EgWRI1). EgWRI1 protein is 93 amino acids shorter than AtWRI1 with low sequence conservation and all deletions occurring in the Cterminal region. We asked whether this divergent EgWRI1 protein, from a non-seed tissue with very high oil content, and from a phylogenetically distant species is able to complement the Arabidopsis loss-of-function mutant wri1-1. We show that expression of EgWRI1 is able to restore several phenotypes of wri1-1, including reduced seed fatty acid content, the “wrinkled" appearance of the seed coat, reduced seed germination, and impaired seedling establishment. Comparison of the protein sequence of WRI1 orthologs across many diverse plant species revealed the conservation of a 9 bp exon encoding “VYL". However, this small exon is missing in one of three predicted AtWRI1 splice forms. To understand expression of WRI1 splice forms we performed RNASeq analysis of Arabidopsis developing seeds and queried other Arabidopsis EST and RNASeq databases derived from a number of tissues and from a range of plant species. In all cases, only splice form 3 is expressed in Arabidopsis and VYL is observed in the cDNA of all WRI1 orthologs investigated. Site-directed mutagenesis showed that amino acid substitutions within the ‘VYL' exon of AtWRI1 results in failure to restore reduced oil content of wri1-1 seeds, providing direct evidence for the crucial role of this small exon in AtWRI1 function.