Microbiotic crusts play an important role in arid and semi-arid regions. Yet, very little information exists regarding the factors that impact their development. In an attempt to assess the main factors that may determine their growth, measurements of the amount of fines (silt and clay), rain, moisture content, wetness duration and wind erosion and deposition were carried out along a 12 station transect within a partially crusted dune field in the western Negev Desert and compared to the crust cover and chlorophyll content. Surface stability was the only variable that exhibited significant relationship with crust cover while daylight wetness duration exhibited strong positive relationship (r2 = 0·92–0·99) with the crust's chlorophyll content. The data point out that microbiotic crusts may serve as a useful biomarker for surface stability. While wetness duration and wind will control crust cover and the crust chlorophyll content in semi-stable habitats (with absolute annual change in sand level of 2–3 mm), stable habitats (absolute change <1 mm) will be controlled primarily by moisture, while habitats with low surface stability (absolute change of tens and hundreds of millimeters) will be primarily controlled by wind. Furthermore, owing to the strong positive relationship between daylight wetness duration and the crust's chlorophyll content, the crust may serve as a useful biomarker for the quantification of surface wetness duration. Copyright © 2009 John Wiley & Sons, Ltd.