Prof Phil Munday (James Cook University) says that this species is only found in the coral Acropora tenuis. PhD student Martin Hing (University of Wollongong) has surveyed coral gobies at Lizard Island for several years and also noted the association.

Marty failed to find most species of Gobiodon following the enormous bleaching event in 2016, presumably because so many corals had died. Gobiodon aoyagii was the exception because Acropora tenuis survived better than other Acropora corals.