Bats are species of high conservation status – subject to Biological Diversity Act, Bern Convention, Bonn Convention, EUROBATS, Habitat Directive, IUCN Red List. Bats are essential for nature. The big sized bats eat various moths and worms that are harmful to agriculture and forestry. The small-sized bats eat mosquitoes and other double-winged insects – carriers of disease such as malaria and leishmania. Bats that eat fruit and flowers disperse seeds of more than 500 species of trees and shrubs and pollinate flowers. Guano, or bat’s droppings, is the highest quality natural fertilizer. It contains much more nitrogen and phosphate than other natural or artifical fertilizers. Considering ecology and distribution of bats in the cross border area their sustainable conservation requires joint actions. Common cross border challenges connected with bats are: increasing use of pesticides in agriculture, which poisons the bats who consume them, disturbance of colonies, particularly by people exploring caves in winter, human presence disturbs hybernating bats, causing bats to loose their energy and leading to exhaustion and death, extermination, hunting. These threats fall within the scope of the cross border challenges for habitats, which are indicated in the Cooperation Programme. The project objectives correspond to the goal of the Programme, which is improving the conservation status of the cross border area habitats.