The Philippine eagle is a sexually monomorphic raptor which lacks the sex-linked morphology determining the gender especially in the juveniles. Thus, a PCR amplification technique was used to determine the sex of 24 eagles at different stages of development (2 to 37 years old) in captivity at the Philippine Eagle Center, Malagos, Davao City. Fractions of the sex-linked genes, CHD-W and CHD-Z of each individual were amplified. Ka Brianne (female) and Jag (male) having 9 offspring conceived through artificial insemination were used as positive controls for sex identification of 22 other individuals. Two individuals of Gallus domesticus with confirmed genders were also included and run through PCR amplification together with the Philippine eagles using primers CHDFORNEW and CHDREVNEW to test the method. Females revealed two district bands (290 bp and 280 bp in size) while the males revealed only a single band of 280 bp. Eleven eagles were found to be females while 13 were found to be males. DNA sexing gave a 100% confirmation of the assigned sexes of the eagles, which were obtained through morphometric analysis done by personnel at the captive breeding center. DNA sexing could be a practical technique in sexing newly hatched eaglet and juveniles, naming of eagles, establishing life history characteristics, and pairing attempt or assignment of partners in the threatened avian species such as the Philippine eagles.