We investigated the structures of ionic liquids (1-butyl-3-methylimidazolium iodide [BMIM][I] and 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM][BF4]) and their aqueous mixtures using attenuated total reflection (ATR) infrared absorption and Raman spectroscopy. The ATR spectrum in the CHx (x = 1, 2, 3) vibration region from 2800 to 3200 cm(-1) was very different between [BMIM][BF4] and [BMIM][I] even though all the spectral features in this region were from the butyl chain and the imidazolium ring of the same cation. The spectrum did not change appreciably irrespective of the water concentration for [BMIM][BF4], whereas the spectrum from [BMIM][I] showed significant changes as the water concentration was increased, especially in CH-vibration modes from the imidazolium ring. For very diluted solutions both aqueous mixtures of [BMIM][I] and [BMIM][BF4] showed very similar spectra. Mixing of [BMIM] [I] with heavy water (D2O) facilitated the isotopic exchange of the proton attached to the most.acidic carbon of the imidazolium ring into deuterium from D2O, whereas even prolonged exposure to D2O did not induce any isotopic exchange for [BMIM][BF4]. Raman spectra around 600 cm(-1) indicative of the butyl chain conformation also changed differently as the water concentration was increased between [BMIM] [I] and [BMIM] [BF4]. These differences are considered to come from the variation in the position of the anion, where I- is expected to be closer to the C(2) hydrogen of the imidazolium cation and interacting more specifically as compared to BF4-.