Beaked whales of the Family Ziphiidae are the least known of all cetacean families. Here, using mitochondrial DNA Control Region and Cytochrome B, and supported by morphological comparisons of skull and teeth, we identified a 4.6 m female beaked whale, stranded in Maco, Compostela Valley, Philippines on December 19 2012, as the Deranayigala's beaked whale, Mesoplodon hotaula. This is the first record of M. hotaula in the Philippines and only the eighth specimen in the world.