The oil palm species, Elaeis oleifera although it produces lower oil yield than its African counterpart Elaeis guineensis, does possess certain unique traits that are of interest to breeders. E. oleifera has slower annual height increment, higher level of carotenoids and unsaturated fatty acids. A number of interspecific hybrid crossing programmes have been initiated to introgress the unique characteristics of E. oleifera into high yielding planting materials. As such, an appropriate backcross interspecific hybrid population (BC2) could be used to develop genetic maps and identify quantitative trait loci (QTL) linked to traits of interest, which will be potentially helpful in reducing the number of breeding cycles. The objective of this study was to determine the heritability of SSR and SNP loci in oil palm. Seventy-five palms from a BC2 population were selected as the mapping population. A total of 4966 (4451 SNP and 515 SSR) markers were screened and 2135 (43%) were polymorphic and mostly contributed by the female parent. The level of polymorphism exhibited by the BC2 population was similar for both marker systems. Genotyping results revealed a sufficient number of co-dominant polymorphic markers that are important in genetic mapping studies. Chi-square test showed that 87.6% of the markers were in accordance to the expected Mendelian segregation ratios. The results indicated that they are stably inherited and suitable for genetic mapping studies and also have proven to be useful as fingerprinting tools to assess the genetic purity in controlled crosses.