We report the coupling of a portable Raman spectrometer to an acoustic levitation device to enable environmental monitoring and the potential taxonomic identification of microalgae. Spectra of living cells were recorded at 785 nm using a fiber-optic probe coupled to a portable Raman spectrometer. The spectra exhibit an excellent signal-to-noise ratio and clearly show bands from chlorophyll a and beta-carotene. Spectra of levitated photobleached microalgae clearly show a reduction in chlorophyll a concentration relative to beta-carotene after 10 min of exposure to a quartz halogen lamp. Spectra recorded from levitated nitrogen-limited cells also show a significant reduction in bands associated with chlorophyll a, as compared to nitrogen-replete cells. To investigate the diagnostic capability of the technique, four species of microalgae were analyzed. Good quality spectra of all four species were obtained showing varying ratios of beta-carotene to chlorophyll. The combination of an acoustic levitation device and a portable Raman spectrometer shows potential as a taxonomic and environmental monitoring tool with direct application to field studies in remote environments.