By far the commonest consituents of insular phosphate deposits are calcium phosphates of the apatite series of minerals, especially varieties that contain structural carbonate in their crystal lattices, e.g. francolite and dahllite. This reflects the fact that the vast majority of described insular phosphate deposits occur in low latitudes, where they have formed, in a tropical environment, by metasomatic replacement of carbonate in coral substrates by phosphate derived either from avian excrement or from phosphorus-enriched lagoonal/lacustrine waters.

Thin, recently-formed guano accumulations on islands of the subantarctic Bounty group differ radically in that they consist principally of struvite, a hydrated ammonium magnesium phosphate that is better known as a component of human/mammalian urinary stones and enteroliths, and of bat guano in sheltered speleothems. Apatite occurs only in an accessory role in the Bounty Islands guano. This contrast in mineralogy, and the somewhat anomalous survival of soft, unstable struvite in a totally exposed environment on the Bounty Islands, are attributed to climatic factors and to the nature of the granodioritic rock substrate.