Photosynthetic microbial communities under translucent rocks (hypolithic) are found in many arid regions. Studies have shown that at the global scale, there has not been intercontinental gene flow, and gene flow between deserts on the same continent has rarely occurred. Few studies have investigated patterns of hypolithic community composition at distances small enough that climatic factors do not vary but great enough to determine whether colonisation occurs as a result of rock to rock dispersal or from the surrounding soil microbial community. We examined hypolithic cyanobacterial diversity in semi-arid Australia, and tested the hypothesis that a sample of rocks along a 10 km transect would reveal substantially higher diversity than had been previously discovered from a limited sample effort from this site. We sampled 6 rocks from each of 4 adjacent 1 m2 quadrats (“distance zero”) and 4 additional quadrats located 10 m, 100 m, 1,000 m and 10,000 m away. A total of 3,108 cyanobacterial OTUs were detected (mean = 580 OTUs per rock). A rarefaction analysis showed a flattening of the curve around 30 samples. Most OTUs were neither widespread nor abundant. However, the few that were widespread tended to be abundant. There was no difference in the community composition between the 4 sites at distance zero, but the sample 10 m away was significantly different, as were the communities at all other distances when compared to distance zero. Substantial numbers of additional OTUs were recorded with increasing distance up to 100 m. These patterns of distribution are consistent with a colonisation model involving dispersal from rock to rock. Overall, our results indicate that distance was a significant factor that can be confounded by inter-rock differences. Most of the diversity was represented in the first 100 m of the transect, with an additional 1.5% of the total diversity added by the sample at 1 km, but only 0.2% added with the addition of the 10 km site.