Radio observations of warm molecular clouds provide a partial picture of their molecular content. Some molecules are observed from the emission of only one rotational line, other from a few, and most of the molecules that probably exist in these clouds are never observed. However, mid and far IR spectroscopy with ISO can provide a full description of the molecular content of the most conspicuous molecular clouds of our galaxy for a moderate cost in observing time. We propose to carry out a full resolution SWS grating survey between 4 and 45 um in some prominent molecular clouds as SgrA, W51-IRS1, NGC6334N, Orion-IRC2, M17, etc (see Table 1). In order to fully explore the infrared spectrum of these conspicuous clouds, we also propose to carry out a LWS fast scanning FP survey in some of these sources. Because of the high kinetic temperature of these clouds we expect to see all the lines in emission for wavelengths above 80-100um. In addition to the molecular content of these warm molecular clouds, the cold dark clouds in their line of sight will also produce strong absorptions. They will be easily recognized from the low number of ro-vibrational lines that will appear and in the case of SgrA because the large velocity shift between it and the local cold dark clouds. The proposed observations will provide a full database of the molecular content of warm molecular clouds and of the local cold dark clouds. The molecular abundances and the physical conditions of the gas will be accurately derived. Hence, these observations will provide an unique check of our current understanding of the chemistry in these objects. In addition to the normal and suspected molecular bands that these clouds will present, many new molecules will be seen. This survey will also provide a detailed database the next two decades for spectroscopic and physical studies of warm molecular cloud. We stress that one of the last unexplored windows of the electromagnetic spectrum of these prototypical clouds will be finally open by the ISO spectrometers.