The behavior of molecules in different atmospheric microwave-induced plasmas (MIPs) has been studied by means of optical emission spectroscopy. This is in order to obtain more insight into molecular processes in plasmas and to investigate the feasibility of emission spectroscopy for the analysis of molecular compounds in gases, e.g. flue gases. Various molecular species (i.e. N2, CO2, H2O, SF6 and SO2) have been introduced into discharges in argon or in molecular gases such as carbon dioxide or nitrogen. The plasmas were created and sustained by a guide-surfatron or a torch in the power range of 150 W to 2 kW. Only nitrogen sometimes yielded observable emission from the non-dissociated molecule (first and second positive system). Using other molecular gases, only dissociation and association products were observed (i.e. atomic species and diatomic molecules such as CN, C2, CO, OH, NH and N2+). The intensities of these products have been studied as a function of the concentration of introduced molecules, the position in the plasma and the composition of the plasma environment. Since in most cases the same diatomic association products are seen, observed associated molecules can only to some extend be related to the molecules originally present in the plasma gas. Therefore, it will be difficult to use atmospheric microwave discharges for the analysis of gas mixtures under the experimental conditions studied.