The fundamental question of why we encounter certain animals in a given place is related to their habitat selection. To study habitat selection, we need to define variables we can measure in the landscape. Conversely, species lists can be suitable for describing the quality of habitats. Different approaches are discussed to analyze the factors that determine the habitat choice of species or individuals, such as correlations, key factor search, and experimental changes. The procedure for using animal focal sampling to analyze habitat use is illustrated with examples. The factors determining habitat selection for a species can also change with the year’s seasons and can also depend on other species. Agroforestry systems are managed to achieve the highest possible biodiversity in land-use systems. The extent to which animals accept agroforestry systems is discussed. If the habitat choice of an animal species is known, its presence can also be used as an indicator for a specific habitat type. We provide examples of bioindication for birds and beetles.