Gas represents the bulk of the mass content in protoplanetary disks. It is therefore observations of gas that can provide important information of physical structure and chemical evolution of disks. This involves a detailed understanding of the spectroscopic signatures of the gaseous components and the conditions under which their excitation occurs. In the following I provide an introduction to the principles of molecular spectroscopy by discussing the spectral signatures of the most abundant molecular species found in protoplanetary disks. The presentation for each molecule is supplemented by an up-to-date discussion of relevant observations and subsequent constraints on the corresponding physical conditions in protoplanetary disks. A primer to excitation diagrams as a simple but effective tool for accessing the excitation of spectral lines is presented towards the end of the chapter.7th Lecture of the Summer School "Protoplanetary Disks: Theory and Modelling Meet Observations"