The genetic purity of a controlled cross is essential for achieving the objectives of a breeding program for any crop. This study evaluated SSR markers for assessing the legitimacy of two oil palm interspecific BC₁ x BC₁ populations, namely, Populations 9 and 10. A total of 40 primer-pairs were screened, resulting in the identification of 19 and 20 informative markers for Populations 9 and 10, respectively. The markers revealed sufficient genetic variation in allele frequency, heterozygosity and polymorphic information content in both populations. The phylogenetic trees revealed three and 32 outliers in Populations 9 and 10, respectively. In addition, the palms originally recorded as parents to the crosses had numerous loci that were mismatched with the non-outlier offspring. We reconstructed the expected genotypes of the real parents based on the segregation profiles observed among the legitimate offspring in the two families, resulting in 100% parent-offspring assignment. This study discusses how the SSR genotypes of palms were examined to detect outliers and to predict the genotypes of the true parents in these interspecific hybrids, the first such report for oil palm. The information will be useful for various controlled crosses of oil palm interspecific hybrids and other outcrossing plant species.