Raman microspectroscopy is a label-free and nondestructive technique to measure the intrinsic chemical profile of single cells. The naturally weak Raman signals hampered the application of Raman spectroscopy for high-throughput measurements. Nearly all photosynthetic microorganisms contain carotenoids that are active molecules for resonance Raman at a 532 nm excitation wavelength. Hence, the acquisition time for a single photosynthetic microorganism can be as short as 1 ms. The carotenoid bands in Raman spectra of photosynthetic microorganisms utilizing (13)CO(2) shifted when compared to the spectra of cells utilizing (12)CO(2). Here, a mixture of (12)C- and (13)C-cyanobacterial cells were counted using a microfluidic-device-based Raman-activated cell counting procedure to prove the concept that Raman spectroscopy can be used as a high-throughput method to profile a cell population.