The assessment of indoor fungal growth has attracted the attention of the research community for many decades. In the effort to assess the fungal burden in the built environment, multiple analysis techniques have been established and offer a plethora of information for the extent of contamination and fungal diversity. However, all analysis techniques are accompanied by drawbacks and the selection of the most appropriate method can become challenging for researchers and practitioners. The aim of this study is to present the most widely used analysis techniques, underline their merits and disadvantages, and provide guidance on the selection process to ensure that the analysis outcomes match the aims of the investigations.