Analysis of Genotyping-by-sequencing data identified 305K species-informative SNPs between Elaeis oleifera and E. guineensis on the E. guineensis 9.1 reference. These SNPs are defined as loci where the frequency of the major alleles in both species are different and have frequency at least 0.97 in their respective species. Here we report 289K species-informative SNPs that were also successfully mapped to the E. guineensis version 5 reference (Table 1) and the for the remaining 16K SNPs, position on the EG9 build is indicated (Table 2). This increased number in the EG9 draft is due to the improvement of the EG9 draft, which incorporates more of the contigs and repeat elements onto the chromosomes, which in turn, improves the mapping and SNP calling on the EG9 draft"