At present, most of the endemic birds are common.
The primary forest specialists on the island are the São Tomé Fiscal Shrike, Dwarf Olive Ibis, Giant Sunbird, Maroon Pigeon, São Tomé Short-tail and the São Tomé Grosbeak. Destruction of even the smallest amounts of the rather limited area of remaining primary forest would jeopardise the future existence of all these species. In addition, the São Tomé Oriole and São Tomé Scops Owl would become seriously endangered if the remaining primary forest was lost. It is of immediate importance that these areas be given protection. At present the forests of the south-western areas are not under threat as access to them is difficult. However destruction is occurring where the forest is close to centres of human population, especially around the northern edge near Lagôa Amélia. The high altitude primary forest at Lagôa Amélia is the stronghold of the Maroon Pigeon and supports populations of the Giant Sunbird, São Tomé Scops Owl and São Tomé Oriole. It is also the area most at threat; agriculture has been encroaching for the last ten years around the Lagôa.
The abandoned plantations have regenerated into secondary forest and provide suitable habitat for several endemic species and also buffers the primary forest from development. Mature secondary forest is especially important for the São Tomé Scops Owl, São Tomé Thrush and Giant Weaver, species which occur at lower densities elsewhere. The owl and thrush are as common in primary forest but a major part of their population would be destroyed if secondary habitats are removed. The Giant Weaver seems to be a secondary habitat specialist. Whilst not totally confined to secondary habitats it would become seriously endangered if all areas of secondary forest were cleared. This habitat also provides a valuable subsidiary habitat for the São Tomé Oriole. The extent of forest regrowth on the island at present and the low exploitation rates mean that it is a relatively secure habitat. BDPA (1985) and Interforest (1990) both recommend that the secondary forest be used as a timber resource and if exploitation is not carefully managed populations of several species could be threatened. If plantations are replanted then this should be done in such a way that the endemic species can exist in them.
Apart from the forest destruction the major problem facing the islands' endemic birds is the removal of shade trees from cocoa and coffee plantations. These crops have been traditionally grown beneath trees whose canopy provides shade. This provides a forest type habitat and provides suitable conditions for many of the commoner endemics, especially the São Tomé Weaver, São Tomé Paradise Flycatcher, São Tomé Seedeater and the São Tomé Sunbird. Our surveys showed that removal of shade trees reduces not only the numbers recorded but also species diversity. Shade trees in plantations are a great source of timber for the islands. If a rotational cut system were adopted with replanting after removal this would provide a sustainable timber resource as well as minimising the damage to the associated bird community.