Macedonia is known for its high level of taxonomic diversity and the high number of relict and endemic species. The country supports 252 known endemic plant species. An estimated 70 species are threatened. Some 30 plant communities are considered endangered and/or threatened. Due to the extremely high biodiversity of the Balkan Region concentrated in Macedonia (70%-90% of all plant species recorded in the Balkans), the country is widely recognized as the most important ‘Biodiversity Hotspot’ of Europe.
According to the World Conservation Monitoring Centre, Macedonia has 414 known species of amphibians, reptiles, birds, and mammals. Of these 4.8% are reported to be threatened.
Although no records on animal species diversity, information on relative abundance and distribution are available for the Bregalnica River Basin District – except for game species subject to controlled and well-regulated hunting- it may safely be assumed that species diversity and relative abundance is highest in the upper and most intact reaches of the river basin. Animal species diversity within the lower river floodplains, which is mostly under intensive agriculture, is believed to be low as a result of early habitat alienation and the past and current liberal and uncontrolled use of agro-chemicals with unknown effects on animal species which have not managed to adapt to cultivated land.
Forest ungulates, common throughout the upper Bregalnica River Basin District, include roe deer, wild boar, and red deer (rare). Typical forest-dwelling furbearers include martens, ferrets, foxes and badgers. River otters are still known to appear in the area. Wolves are relatively common throughout the area in spite of heavy hunting pressure. Upland game birds of the target area include grouse, chukar partridge, quail, pheasant, and dove. Waterfowl hunted in the target area includes several duck species, coots, cormorant and snipe.
The Ichthyofauna is represented by species, such as chub, barbel, and dace. Less common are the common carp and catfish. Stocks of native trout and most of the other edible fish species are low as a direct result of extremely high water contamination of the dams and River Bregalnica itself, and because of over-fishing.
To date there are no comprehensive research data on plant species composition and distribution, and only rudimentary information on the habitat types in Bregalnica River Basin are available. The highly diverse topography, relief, geology, soils, water distribution and the numerous micro-climates typifying the Bregalnica River Basin however suggests the occurance of a very high plant species diversity.
Several endemic vascular plant species have been recorded in the Bregalnica River Basin which is also well known for its high diversity of “medicinal” and aromatic plant species widely collected and used by local people. In addition, twenty-five tree species, with multiple sub-species are known to be present. Over 50% of the river basin, mostly in its upper part, is covered by forests (136,738 ha), dominated by mixed stands of oak and beech. Coniferous forests, composed of pine, silver fir and spruce, are rare. The habitat type of dry meadow is found mostly on flat slopes of southern exposure. Sub-alpine meadows, typically rich in herbs and grass species, cover the higher mountains of the upper part of the Bregalnica River Basin District.