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Abstract. In order to understand how communities of rock‐inhabiting micro‐organisms are spatially organized, rock samples and environmental variables were collected from five cliff sites in Ontario, Canada. Algae and cyanobacteria were extracted from the epilithic zone (rock surface) and endolithic zone (subsurface) of 180 samples, and the frequency of each taxon (genus or larger) was determined. Multivariate statistical analyses were used to determine (1) the variation in community composition on different spatial scales; (2) differences in community composition between surface and subsurface; and (3) the environmental constraints of community structure. 13 taxa of cyanobacteria and 12 taxa of eukaryotic algae were identified in the endolithic zone, and 17 and 14 in the epilithic zone, respectively. The most frequent taxa were similar in both zones, but MANOVA of species frequencies showed significant differences between endolithic and epilithic communities. DCA and CCA showed that geographic‐scale variation in community composition was the dominant trend in the data for both surface and subsurface. Cyanobacteria and eukaryotic algae showed a clear separation on the first ordination axis. When the geographic‐scale variation was removed in a partial ordination, the separation of organisms by kingdoms disappeared and epi‐ and endolithic ordinations were no longer similar. Light then appeared to control the endolithic species composition, while other factors, possibly moisture‐related, were suggested for the epilithic community. Despite biomass and productivity that varies mostly at scales of < 1m2, we conclude here that species composition and its environmental constraints vary at small as well as larger scales.

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