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Floristically Bwindi is amongst the most diverse forests in East Africa. More than 1,000 flowering plant species, 324 tree and shrub species and more than 104 species of ferns have been identified.

The northern (low altitude) sector is rich in species of the Guineo-Congolian flora. These include two species internationally recognised as endangered, Brown mahogany (Lovoa swynnertonii) and Brazzeia longipedicellata (Hilton-Taylor, 2002).

Ten tree species occur nowhere else in Uganda: Allanblackia kimbiliensis, Brazzeia longipedicellata, Chrysophyllum pruniforme, Croton bukobensis, Grewia mildbraedii, Leplaea mayombensis, Maesobotrya purseglovei, Melchiora schliebenii, Strombosiopsis tetrandra and Xylopia staudtii. Species such as Allanblackia kimbiliensis, Brazzeia longipedicellata, Dicranolepis incisa, Milletia psilopetala and Sampium leonardii-crispi need special attention because they are found in only one other country in addition to Uganda. Allanblackia kimbiliensis, Dicranolepis incisa and Sampium leonardii-crispi have been recorded in Congo in addition to Uganda while Brazzeia longipedicellata, Milletia psilopetala have been recorded in Congo.

Common canopy species include: Chrysophyllum gorungosanum, Entandrophragma excelsum, Newtonia buchananii, Parinari excelsa, Podocarpus milanjianus, Prunus africana and Symphonia globulifera. Less common distinctive species include: Allanblackia floribunda, Balthasaria schliebenii, Ekebergia capensis, Ocotea usambarensis and Zanthoxylum gilletii.

Typical sub-canopy trees include: Albizia gummifera Allophylus abyssinicus, Beilschmiedia ugandensis, Carapa grandiflora Cassipourea ruwensorensis, Croton macrostachys, Dichaetanthera corymhosa , Dombeya goetzenii, Drypetes gerrardii, Faurea saligna , Ficalhoa laurifolia, Leplaea mayombensis, Harungana madagascariensis, Ilex mitis, Macaranga kilimandscharica, Neoboutonia macrocalyx, Olea capensis, Olinia usambarensis, Polyscias fulva, Strombosia scheffleri, Syzygium guineense and Tetrorchidium didymostemon.

Common understorey species include: Allophylus macrobotrys, Cyathea deckenii, Psychotria mahonii, Lobelia giberroa, Myrianthus holstii, Rytigynia sp, Tabernaemontana holstii, Teclea nobilis and
Xymalos monospora.