The Raman spectra of cyanobacterial species, Gloecapsa and Nostoc, in clear gypsum crystals from the Haughton Crater, Devon Island, Canadian High Arctic, site of a meteorite impact during the Miocene some 23 Mya, have been recorded using several visible and near-infrared excitation wavelengths. The best spectra were obtained using a green wavelength at 514.5 nm and a confocal microscope with an image footprint of about 2 m in diameter and 2 m theoretical depth. Raman biosignatures for beta-carotene and scytonemin were obtained for one type of colony and parietin and beta-carotene for another; chlorophyll was detected in both types of colony. The different combination of these radiation protectant biomolecules suggests that the two cyanobacterial colonies, namely Nostoc and Gloecapsa, are adopting different survival strategies in the system. Confocal spectroscopic probing of the gypsum crystals exhibited sufficient discrimination for the identification of the biomolecules through the gypsum crystal, in simulation of the detection of extant or extinct halotrophs. This supports the viability of Raman spectroscopic techniques for incorporation as part of the instrumentation suite of a robotic lander for planetary surface exploration for the detection of organisms inside sulfate crystals from previous hydrothermal activity on Mars.