Oil palm has a narrow genetic diversity due to intensive selection in breeding. Loss of diversity in breeding materials can lead to many consequences, despite uniformity is critical to breeders. The objectives of the study are to evaluate the genetic diversity in Deli and AVROS populations, and to determine the levels of inbreeding using CIRAD’s Simple Sequence Repeat (SSR) markers. The parental populations evaluated were 186 palms from Deli and 188 palms from AVROS progenies sourced from two agencies. Genotyping using 32 SSR markers produced 230 alleles among the 17 oil palm progenies. The number of alleles scored ranged between 4 to 11. The average number of alleles per locus was 7.1875. The expected heterozygosity (He) and observed heterozygosity (Ho) were 0.7063 and 0.5270, respectively. The dendogram revealed that the 17 populations were clustered into three main clusters namely Deli dura, AVROS and Ekona populations. The two different generations of AVROS resulted in Genting AgTech Sdn Bhd (GAT) AVROS had inbreeding coefficient of 0.0336 compared to Department of Agriculture (DOA) Sabah AVROS which was -0.0810. The diversity revealed via SSR showed that there are still present of variability in some of the progenies. The inbreeding level can serve as guidance during the inbred lines development.