Deep UV resonance Raman micro-spectroscopy (lambda(exc) = 244 nm) was applied for a highly sensitive, selective, and gentle localization of the antimalarial quinine in situ in cinchona bark. The high potential of the method was demonstrated by the detection of small amounts of the alkaloid in the plant material without any further sample preparation, where conventional (non-resonant) Raman microscopy was unsuccessful due to a strong fluorescence background. The resonance Raman spectrum of cinchona bark corresponds well with that of quinine; it can be distinguished from its diastereomer quinidine via the mode at 831 cm(-1), which is shifted to 843 cm(-1) in the case of quinidine. This vibration involves a bending motion within the side chain around the chiral center of quinine. Vibrations belonging to the quinoline ring (important for its antimalarial activity in forming pi-pi-interactions to hemozoin) and the vinyl group are resonantly enhanced in the UV Raman spectra. A convincing mode assignment is derived by means of a combination of NIR Raman spectroscopy and DFT calculations. The Raman spectra of quinine in cinchona bark are modeled by considering a hydrous environment that causes a shift of the band at 1362 compared with 1371 cm(-1) in anhydrous quinine. This intense vibration is therefore sensitive to the presence of an aqueous environment and is assigned mostly to a stretching motion within the quinoline ring. The presented results nicely show the sensitivity of Raman spectroscopy to monitor subtle differences within the molecular structure and the influence of a biological relevant hydrous environment and trace low concentrated pharmaceutical relevant active agents in plant material.