We have constructed a 1064 nm deep near-infrared (NIR) excited multichannel Raman microspectrometer using an InP/InGaAsP multichannel detector. This microspectrometer achieves high sensitivity suitable for in vivo measurements of single living cells with lateral resolution of 0.7 mu m and depth resolution of 3.1 mu m. It has been applied to the structural analysis of living cyanobacterial cells, well-known model organisms for photosynthesis research, which are too photolabile to be measured with visible laser excitation. High signal-to-noise ratio (SIN) Raman spectra have been obtained from carotenoid, chlorophyll a, and phycocyanin in a single living cyanobacterial cell with no appreciable interference from autofluorescence or photodamage. Sub-micrometer mapping of Raman intensities provides clear distribution images of the three pigments inside the cell.