In November-December 1990, dugongs, sea turtles and cetaceans were counted from the air at an overall sampling intensity of 9% over a total area of 31288 km2 in the Great Barrier Reef region north of Cooktown. This survey was a repetition of the surveys conducted in 1984 and 1985. The population estimates for dugongs and sea turtles were corrected for perception bias (the proportion of animals visible in the transect which are missed by observers), and standardised for availability bias (the proportion of animals that are invisible due to water turbidity) with survey and species-specific correction factors. The estimates for cetaceans were corrected for perception bias only. The minimum population estimate for dugongs for the survey area in November-December 1990 (10471± s.e. 1578 dugongs), was not significantly different from the estimate for the same region in November 1985 using the same aerial survey technique (8110 ± s.e. 1073). The results of the two surveys for each survey block were remarkably consistent suggesting that the dugong population in the region is stable. However, the technique is not capable of detecting local declines in abundance unless they were considerable. Most of the turtles sighted during this survey were probably large green turtles. The population estimate for the northern Great Barrier Reef region in November-December 1990 was 45644 ± s.e. 3501 turtles compared with 32187 ± 2532 for the same region in November 1985. This difference between surveys was not significant when sighting conditions were taken into account. However, the agreement between the 1985 and 1990 surveys was not nearly as good for turtles as for dugongs, probably due to: (1) the sensitivity of turtle sightings to small changes in sighting conditions which cannot be completely removed in the analyses and (2) the tendency of turtles to migrate to breed coincident with the timing of the surveys. All the cetaceans sighted were dolphins. Most of the animals appeared to be bottlenose dolphins, Tursiops truncates, or Indo-Pacific humpback dolphins, Sousa chinensis. The population estimates for November-December 1990 sum to 4875 ± s.e. 500 dolphins for the whole region compared with 6609 ± 667 in November 1985. The difference in dolphin distribution was significantly different between the two surveys.