Cave habitats represent a unique ecosystem characterized by fairly stable physical and chemical parameters. They are considered an extreme habitat of constant darkness, low temperature, high humidity and low nutrients resulting in small amounts of organic carbon, a key component of life. Much research in recent decades confirms significant advances in the understanding of subterranean biology, and subterranean ecology in particular. However, we are still far from understanding fundamental issues such as adaptive mechanisms, species distribution patterns, trophic interactions, and ecosystem functioning. Underground fauna and habitats are an important component of world and European natural heritage. At the core of ecosystem conservation, management and restoration lies continuous monitoring of the state of change. The research in the Krka National Park was carried out in the period from March 2015 to October 2016, with field work in each season (spring, summer, autumn, winter). This thesis analyzes the temporal and spatial changes in the composition and diversity of fauna, as well as the effect of different sampling methods used. The similarities and differences of the same microhabitats in different speleological objects were analyzed. The plot census method is suitable for larger caves, while for simpler caves the object census method can be applied. Numerical data on composition and abundance provide insight into the current state of fauna and continuous monitoring is the only way to record changes in populations.