Haploid technology facilitates the production of completely homozygous plants that are desirable in crop breeding. Having just one complete set of chromosomes in a haploid individual allows it to be doubled to produce a normal but pure 2n diploid plant. Here, we report a simple way to identify natural haploids of oil palm (Elaeis guineensis Jacq.) from screening 6400 abnormal germinated seeds. Initially, the germinated seeds were selected based on 12 unique ‘off-type’ morphological characteristics. The selected seeds were then grown and the seedlings were subjected to a second selection for three distinctive characteristics. Ploidy analysis with flow cytometry (FCM) and chromosome karyotyping confirmed the haploidy of one seedling with stunted height and size. Further analysis with the True-to-Type single nucleotide polymorphism (SNP) panel demonstrated that the plant was homozygous at all the loci tested, confirming its haploid status. This study has established a simple and systematic strategy that assists in accelerating early identification of oil palm spontaneous haploid.