The tune is supposed to be that of an old Spanish song.
"Sound Off!," Edward Arthur Dolph, 1929 (1942) has the opinion of those who served there in the period of the Spanish American War:

Zamboanga, Mindanao,
From the transport you look damn well,
But before I'd serve again in Zamboanga,
I'd rather serve a hitch in Hell.

Gern is quite correct, the song refers to the natives of Zamboanga, some of whom, among the Muslims, are still guerillas fighting for independence.

Dolph comments that stanzas have been added ad libitum to the song.
Most verses have more emphasis than those in the book of Navy songs, which is from the Navy rather than the Army point of view, and adds verses about navy efforts in other areas.

Oh, the carabao has no hair in Mindanao,
Oh, the carabao has no hair in Mindanao,
Oh the carabao has no hair--
Holy Smoke! But he is bare!
So the carabao has no hair in Mindanao.

"Oh, the Moros have no tails in Zamboanga" was the first line sung by the troops.

Zamboanga is now called "The City of Flowers" and tries to attract tourists.