Abstract: The application of wholemount clearing techniques with different clearing agents and clearing methods in plant biology are illustrated by three examples: measuring lateral root primordium number in tomato (Lycopersicon esculentum), recognizing compatibility between pollen of common goldenrod (Solidago decurens) and the stigma of goldenrod (S. canadensis), and observing the development of the ovule of Conyza sumatrensis. This article reviews applications in plant biology research, especially of plant reproduction biology, and advantages and disadvantages of the whole clearing techniques. Some technique details such as the choice and use of clearing agents and association with specific microscopes are discussed.