The Great Barrier Reef Zoning Plan (2003) came into force on 1 July 2004 and greatly increased the proportion of habitats in the Marine Park protected from extractive uses, most notably from commercial and recreational fishing. Since the increase in habitat protection was designed to enhance the conservation of marine biodiversity, including fish stocks, all stakeholders are interested in the response of populations to the zoning changes. In 2005–2006, the AIMS Long-term Monitoring Team reported that the most important commercial fish species, coral trout, had increased in abundance by about 50% on mid- and outer-shelf reefs after less than two years of the cessation of fishing. A partnership team from James Cook University reported almost exactly the same result from inshore coral reefs. While it could be assumed that these two studies are representative of all habitats, GBRMPA acting through the Marine and Tropical Sciences Research Facility (MTSRF) requested explicit evidence that the new zoning has enhanced the stocks of fish species such as the iconic red emperor and two species of nannygais found on deep shoal habitats.

Unlike emergent shallow reefs, which are recorded accurately on navigation charts, there is much less public knowledge about deep shoals and the best information is often closely guarded by those who fish them. In the last 12 months, with support from the MTSRF programme, AIMS has been locating shoals using multi-beam swathe mapping in collaboration with James Cook University and establishing the abundance of fish populations on these deep habitats below diving depth using non-destructive video surveys.

Preliminary results show that red emperors and nannygais use a range of shoal habitats at different stages in their life cycle. Sub-adults (below legal capture size) are abundant on low relief epibenthic gardens common on the coastal side of the Great Barrier Reef Lagoon while adults prefer deeper and more structured habitats further offshore. Like all schooling species, these fish are mobile and patchy in abundance, which makes it challenging to assess their abundance in different zones of the Marine Park. Nonetheless, baseline data have been captured in the last 12 months from several large offshore banks in different habitat protection zones where adults are persistent and these populations can now be tracked over time to reveal the effect of fishing upon their local abundance.

Red emperor feeding at a bait station.