The AIMS Long Term Monitoring Program (LTMP) has been monitoring fish populations on the Great Barrier Reef for over a decade. The work has revealed strong spatial patterns in GBR fish communities with distinct inshore, mid-reef and outer shelf communities. These communities also vary with latitude within the area monitored – between Lizard Island and the Capricorn Bunker reef system. Unless there is a major disturbance such as a cyclone, an outbreak of Crown of Thorns Starfish or major coral bleaching that causes changes in the benthic community, the fish communities on each reef change little through time.

Early survey work identified key regions of biodiversity to advise theGreat Barrier Reef Marine Park Authority's Representative Areas Programand the subsequent rezoning of the GBR marine park in 2004. The LTMP is now involved in monitoring the effects of zoning on target fish species such as coral trout and biodiversity in general. Their findings suggest that the size and density of coral trout has increased in protected areas compared with reefs that are open to fishing.

Deep water habitats are increasingly targeted for fishing as new technologies make these areas more accessible. Deeper water fish communities are monitored by AIMS using Baited Remote Underwater Video cameras (BRUVs). New insights provided by these systems help managers identify areas that need protection.

Monitoring reef fish and studying larval fish distribution also helps AIMS scientists understand the effect of large scale environmental factors such as climate change and ocean currents on reef fish populations and ecology.