Six microsatellite markers obtained from Canarium album and Carica papaya detected eight loci in the pili (Canarium ovatum Engl.) accessions with two markers, CasC120 and SSR38, each amplifying two loci. A total of 43 alleles (5.38 alleles per locus) were detected in the 79 pili accessions assayed, while only 3.25 alleles per locus were obtained in Canarium luzonicum and in seven pili varieties registered with the National Seed Industry Council (NSIC). Polymorphism information content (PIC) values of the markers were relatively high across accessions (0.57) and varieties (0.45), indicating the ability of the markers to detect genetic diversity in the population assayed. Gene diversity was relatively high in the pili varieties (0.50) and in the 79 pili accessions (0.62) analyzed in the study, indicating recombination by cross pollination. Cluster analysis grouped the pili accessions and the seven varieties into two clusters. Group I was composed of accessions PDF65 and PDF20, while the other 77 accessions, including the seven pili varieties, clustered together forming Group II. Six of the varieties (‘Katutubo’, ‘Lanuza’, ‘Magayon’, ‘Magnaye’, ‘Mayon I’, and ‘Orolfo’) formed one sub-cluster under Group II, while ‘Laysa’ formed a different sub-cluster. Moreover, cluster analysis of the pili varieties and C. luzonicum showed the same trend wherein the six varieties formed one cluster, while ‘Laysa’ diverged from the group. DNA fingerprints of the pili accessions were generated from the banding patterns observed across the eight loci. The pili varieties gave unique DNA fingerprints, demonstrating the utility of the markers for varietal identification. This is the first report of a study in the Philippines on the molecular characterization of C. ovatum using DNA markers.