Grows best in undulating terrain in the moister lowland tropics, being found at elevations of 0 – 1,700 metres. It prefers an annual rainfall of 1,500 – 6,500 mm, a mean annual maximum temperature of 22 – 28c and a mean annual minimum temperature of 14 – 21c. Prefers heavy soils developed from gneiss and other metamorphic rocks, but it also grows well on sandy loams developed from sandstone. The extremely high prices paid for high quality agar wood and for the essential oil and the indiscriminate felling of both diseased and healthy trees threaten natural stands of Aquilaria malaccensis to extinction.

Research into possibilities of artificial induction and stimulation of agar wood formation is therefore urgently required and may offer high economic returns, especially as trials indicate that management of plantations presents no great difficulties. Unless such methods are developed, Aquilaria malaccensis may soon be extinct. Plantations have been established, mainly for experimental purposes, to test methods for the induction of agar wood formation.

Three closely related species of Aquilaria are considered to be the major sources of agar wood and are distinguished by the length of their calyx lobes:- Aquilaria crassna, which comes from Indo-China, has lobes 12 – 15mm long. Aquilaria malaccensis, from India, and Malaysia has lobes 2 – 3mm long. Aquilaria sinensis, from China, has lobes 8mm long.

Flowering and fruiting may start at an age of 4 – 5 years. Good seed years occur infrequently and a medium sized tree may then produce 1.5 kg seed. The best agarwood yields are from trees of 50 years age or more but resin is produced as early as 20 years. Agar wood formation is a pathological process taking place in the stem or main branches where an injury has occurred. Fungi are involved in the process, but the process itself is not yet fully understood. Damage by boring insects is often associated with the infection.

It is believed that the tree is first attacked by a pathogenic fungus, which causes it to weaken. Infection by a second fungus causes the formation of agar wood, but it is unclear whether it is a product of the fungus or the tree. The fungus implicated in the formation of agar wood in this species is Cytosphaera mangiferae, while Melanotus flavolives is assumed to play a similar role in Aquilaria sinensis. This species forms an association with endotrophic mycorrhizal fungi.