The fats, protein and carbohydrates afforded by tree nuts and fruits are key resources for communities from Southeast Asia, through Melanesia, Australia and across Oceania. They are important in long‐distance marine trade networks, large‐scale ceremonial gatherings, and are core resources in a wide range of subsistence economies, including foraging systems, horticulture and swidden agriculture. Recent archaeobotanical evidence has also shown their deep‐time importance, being amongst the earliest foods used in the colonisation of novel environments in Australia and New Guinea, as well as the later colonisation of Near and Remote Oceania. The archaeobotanical methods used to identify fruit and nut‐derived plant macrofossils have been largely limited to use of morphological characters of near whole or exceptionally preserved remains, most commonly endocarps, the hard, nutshell‐like interior layer of the fruit protecting the seed. Here we detail how anatomical characteristics of endocarps, visible in light and scanning electron microscopy (SEM), can be used with surviving morphological features to identify confidently the use of key Asia‐Pacific economic trees, in this case, Canarium, Pandanus and Terminalia. Systematic anatomical description allows the identification of these important economic taxa, and separation from the remains of others such as Aleurites and Cocos, when found in a range of archaeological assemblages. This includes the often highly fragmented charred assemblages that can be recovered routinely from most sites with appropriate fine‐sieving and flotation methods. These methods provide the basis for a more representative and nuanced understanding of ancient plant use, economy and social systems operating in the region and, being particularly useful in tropical regions, will broaden the archaeobotanical database on ancient foods globally.