<p>The rapid evolution of next-generation sequencing (NGS) technology has opened new avenues for genomic research in oil palm, where the shift of single nucleotide polymorphism (SNP) technology from array to genotype-by-sequencing (GBS) is pronounced. In this study, we explored the widely used GBS approach, known as targeted GBS or amplicon sequencing, by verifying the transferability of 384 representative SNP markers from the HD SNP array. A series of evaluations were performed to ensure the reproducibility of genotypes and their allelic frequencies across several genotyping platforms. High reproducibility of scorable genotype calls was observed between replicates within the same targeted GBS dataset, namely Genotyping-in-Thousands by sequencing (97.2–98.2%) and was comparable to another similar platform, deep True-To-Type (73.3–100.0%). Its reproducibility recorded 94.7–98.3% in comparison with SNP array. The small differences were due to only one allele was captured by targeted GBS. Using the finalized 206 SNP markers, numerous trisomy signals were observed among the off-types in the nursery and open field, which require further validation. Interestingly, one off-type seedling has been validated as a triploid aberrant with trisomy observed across its 15 chromosomes. Such cross-platform evaluations are a useful guide for migrating, comparing or integrating SNP data generated by different genotyping platforms, which is expected to be routinely implemented by the oil palm research community as well as other crop systems.</p>