Larval fishes of 96 families were represented in plankton samples taken in four seasons in 1979-80 and three seasons in 1981-82 from 11 sites in the Lizard Island region of the Great Barrier Reef lagoon. Relatively few families dominated the catch: Apogonidae, Gobiidae and Pomacentridae constituted 53-76% of all larvae, depending on site. Several taxa including Labridae, Scaridae, Scorpaenidae, Serranidae and Synodontidae that were rare in previous larval fish studies were relatively abundant in open waters of the Great Barrier Reef lagoon.

Lagoonal and downwind sites in shallow water around Lizard Island had low proportions of old larvae, but the windward site had relatively high values for several families. Sites in the deeper, more open waters of the Great Barrier Reef lagoon generally had higher proportions of old larvae of most taxa in 1981-82 than did the Lizard Island sites in 1979-80.

Although there were seasonal differences in larval fish assemblages, within any season there were only two or three assemblages in the study area. An assemblage dominated by pomacentrids, mullids, tripterygiids, apogonids and blenniids occupied a relatively small area of shallow water near Lizard Island reefs: in Lizard Lagoon, always on the windward side, and often on the downwind side. Another assemblage dominated by apogonids, gobiids, pomacentrids, labrids and engraulids occupied a very large area between Lizard Island and the outer barrier reefs, and occasionally on the downwind side of Lizard Island. Occasionally, a third distinct assemblage, dominated by scorpaenids, gobiids, callionymids, apogonids and engraulids, occurred on the downwind side of Lizard Island. Variability in assemblages at the downwind site was probably due to currents less favourable for retention of larvae than those at the other Lizard Island sites.