The genetic diversity and relationships among the Philippine Mallard, Khaki Campbell and Pekin ducks were analyzed by employing 28 microsatellite primers which were amplifed from the genome of 30 animals representing each genetic group. Twenty-one of the 28 microsatellite primers employed are polymorphic. The average observed and eﬀective number of allele ranges from 2.238 to 2.714 and 1.565 to 1.934, respectively, while the average observed and expected heterozygosity ranges from 0.297 to 0.432 and 0.308 to 0.422, respectively. The within population inbreeding estimate among the three genetic groups of mallard ducks is -0.0020 while the total inbreeding estimate is 0.1292 suggesting that random genetic drift could be happening in the duck populations considered. On the other hand, the measurement of population diﬀerentiation has a value of 0.1309. Relationship analyses reveal that the Philippine Mallard is genetically closer to the Khaki Campbell (0.0944) than with the Pekin (0.1523). The genetic distance between the Khaki Campbell and the Pekin is 0.1386.