About 4,500 species of vascular plants have been recorded in Uganda. The Imatong Mountains have a rich biodiverse flora with much endemism; 1145 species of vascular plant have been recorded here including 110 species of fern. The plains and the lower parts of the mountains are covered by deciduous woodland, wooded grassland and bamboo thickets, while the areas to the east and southeast are in the rain shadow of the mountains, with dry sub desert grassland or deciduous or semi-evergreen bush. The plant diversity of the mountains is due to their position between the West African rain forest, the Ethiopian plateau and the East African mountains, coupled with their relative isolation for long periods during which new species could emerge. Vegetation in the lower areas includes woodlands of Albizia and Terminalia, and mixed Khaya lowland semi-evergreen forest up to 1,000 metres (3,300 ft.). Above 1,000 metres (3,300 ft.) there is montane forest with Podocarpus, Croton, Macaranga and Albizia up to 2,900 metres (9,500 ft.). At the highest levels, the forest is replaced by Hagenia woodland, Erica (heather) thicket and areas of bamboo.

In the northwest of the country, in the Murchison Falls National Park, 80% of the tree cover has been lost over several decades and the remaining woodland is dominated by Terminalia schimperiana and Prosopis Africana, the balance being created by herbivores, which suppress regeneration, and fires which favour fire-tolerant species.[6] In the Semliki National Park in the west of the country, the vegetation is predominantly medium altitude moist evergreen to semi-deciduous forest with Cynometra alexandri being the dominant species of tree.

In the east, Mount Elgon has several vegetation zones. At lower altitudes there is montane forest with Olea hochstetteri and Pouteria adolfi-friedericii, which give way to Afrocarpus gracilior and olive forest at higher altitudes. Higher still, there is a zone of Afrocarpus and the bamboo Yushania alpina, and the summit moorland has tussock grasses, heaths, low herbs, giant lobelias

Uganda has a wide variety of different habitats, including mountains, hills, tropical rainforest, woodland, freshwater lakes, swamps and savanna with scattered clumps of trees. The country has a biodiverse flora and fauna reflecting this range of habitats and is known for its host of primates, including gorillas and chimpanzees. There are ten national parks and thirteen wildlife reserves; some 345 species of mammal and 1020 species of bird have been recorded in the country.

Uganda is a large country in East Africa lying on the equator. It is bounded by the Democratic Republic of the Congo to the west, South Sudan to the north, Kenya to the east and Rwanda and Tanzania to the south. Three large lakes, Lake Victoria, Lake Edward and Lake Albert lie on the borders and Lake Kyoga lies in the centre. The country forms part of the Lake Victoria Basin and consists mainly of a plateau about 1,000 m (3,300 ft.) above sea level. Higher land in the southwest rises to the Rwenzori Mountains on the border with Rwanda, while on the eastern border are a chain of mountains, the highest point being the shield volcano of Mount Elgon (4,321 m (14,177 ft.)). The Imatong Mountains lie on the northern border with South Sudan. Nearly one-fifth of the country is open water or swampland. Lake Victoria is drained by the River Nile which flows through the even shallower Lake Kyoga, part of a complex of periodically flooded lakes and swampland, Lake Opeta forming a separate lake during the dry season. Lake Albert and Lake Edward are deep water lakes lying in the Albertine branch of the Rift Valley.