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Biological soil crusts (BSCs) are ubiquitous communities of diminutive organisms such as cyanobacteria, green algae, lichens, mosses and others associated closely with particles of surface soil, forming a cohesive thin horizontal layer. The ecological roles of BSCs affecting soil nutrient cycling, stability and hydrological processes, influencing the germination and establishment of vascular plants, and serving as habitats for numerous arthropods and microorganism have been well documented. We tested the hypothesis that micro-geomorphological features determine the spatial distribution of BSCs by reallocating related abiotic resources at small- and medium-scales in the Tengger Desert. Our results showed that higher soil pH and higher total potassium content in topsoil positively correlated with the colonization of cyanobacteria and algae in the earliest successional stages of BSCs, while increasing dust deposition onto the topsoil enhanced the development of lichen and mosses in the later stages of BSCs. Increasing soil moisture raised the proportion of mosses and lichen in BSCs, this will possibly change the ecological functions of BSCs, such as nitrogen-fixation by cyanobacteria, clue to the conversion from a complex to relative simple type of BSC. Micro-geomorphology has created various habitats at a small-scale affecting colonization and development of cryptogams. This paper considers the contribution of micro-geomorphology to biodiversity in the extreme and desert systems. Copyright (C) 2010 John Wiley & Sons, Ltd.