We report the effects of electrochromic coloration on the Raman spectra of sputtered a-MoO3 films. The Raman spectra of as-deposited films show two strong peaks at 828 and 951 cm(-1) due to vibrations of the O-Mo6+-O and Mo6+=O bonds, respectively. A shoulder on the right side of the Raman peak at 951 cm(-1) is observed, and we attribute it to the Mo6+=O bonds which originate from the singly coordinated oxygen atoms in alpha phase layered MoO3. When lithium (or hydrogen) ions and electrons are intercalated into a-MoO3, the overall Raman intensity decreases due to electrochromic coloration and an extra Raman peak due to the bonds between Mo5+ and oxygen atoms appears at similar to 400 cm(-1). In addition, the force constant for the O-Mo6+-O bonds increases due to the compressive stress induced by lithium (or hydrogen) ion insertion. We conclude the Mo5+ states are generated as a result of the reduction of the Mo6+ states with ion/electron insertion and the optical absorption in the colored state is caused by transitions between the Mo6+ and Mo5+.