The majority of biomass in the McMurdo Dry Valleys of Antarctica occurs within rocks and soils, but despite the wealth of biodiversity data very little is known about the potential functionality of communities within these substrates. The putative physiological capacity of microbial communities in granite boulders (chasmoendoliths) and soils of a maritime-influenced Antarctic Dry Valleys were interrogated using the GeoChip microarray. Diversity estimates revealed surprisingly high diversity and evenness in both communities, with Chlorobi and Deinococci in soils accounting for major differences between the substrates. Autotrophs were more diverse in chasmoendoliths, and diazotrophs more diverse in soils. Both substrates revealed a previously unappreciated abundance of Halobacteria (Archaea), Ascomycota (Fungi) and Basidiomycoyta (Fungi). The fungi accounted for much of the differences between substrates in metabolic pathways associated with carbon transformations, particularly for aromatic compounds. Nitrogen fixation genes were more common in soils, although nitrogen catabolism genes were abundant in chasmoendoliths. Stress response pathways were more diverse in chasmoendoliths, possibly reflecting greater environmental stress in this exposed substrate compared with subsurface soils. Overall diversity of stress-tolerance genes was markedly lower than that recorded for inland locations where environmental stress is exacerbated. We postulate that the chasmoendolithic community occupies a key role in biogeochemical transformations in Dry Valley systems where granite substrates are abundant among open soils. The findings indicate that a substantial upward revision to estimates of biologically active surfaces in this system is warranted.