Recent significant examples of fluorescence spectroscopy and imaging applications in plant science are reported. Particular emphasis has been placed on the non-destructive fluorescence detection of plant polyphenolic compounds and of plant stress indicators. These techniques could be fruitfully applied in agriculture to control plant diseases and stress conditions avoiding crop yield losses and to assess the quality of vegetable and fruit products. The aim of this chapter is to stimulate the younger researchers in photobiology to better understand the advantages and limits of the different in planta fluorescence techniques available, for their correct applications.