The Mojave Desert has been long considered a suitable terrestrial analogue to Mars in many geological and astrobiological aspects. The Silver Lake region in the Mojave Desert hosts several different rock types (talc, marble, quartz, white carbonate and red-coated carbonate) colonized by hypoliths within a few kilometres. This provides an opportunity to investigate the effect of rock type on hypolithic colonization in a given environment. Transmission measurements from 300 to 800 nm showed that the transmission of blue and UVA varied between rock types. The wavelength at which the transmission fell to 1% of the transmission at 600 nm was 475 nm for white carbonate and quartz, 425 nm for red-coated carbonate and talc and 380 nm for marble. The comparative analysis of the cyanobacterial component of hypoliths under different rocks, as revealed by sequencing 16S rRNA gene clone libraries, showed no significant variation with rock type; hypoliths were dominated by phylotypes of the genus Chroococcidiopsis, although less abundant phylotypes of the genus Loriellopsis, Leptolyngbya and Scytonema occurred. The comparison of the confocal laser scanning microscopy-λ (CLSM-λ) scan analysis of the spectral emission of the photosynthetic pigments of Chroococcidiopsis in different rocks with the spectrum of isolated Chroococcidiopsis sp. 029, revealed a 10 nm red shift in the emission fingerprinting for quartz and carbonate and a 5 nm red shift for talc samples. This result reflects the versatility of Chroococcidiopsis in inhabiting dry niches with different light availability for photosynthesis.