- Abstract Biological Soil Crusts (BSCs) are critical components of desert ecosystems worldwide. While all BSCs significantly modify the surfaces they occupy, the manner in which they affect their environment depends on the composition of the microphytic community. The aim of this paper is to study the hyperspectral thermal emissivity signatures of BSCs in order to identify and characterize them in a sand dune environment. The research was conducted in the northwestern Negev dunes. Measurements of several types of BSCs and bare soil were obtained using ground hyperspectral thermal sensors. We present an ability to spectrally separate different types of BSCs from bare sand, and to rank them according to successional development. Based on this ability, we created a spectral index for the discrimination of sand and BSCs of different types and applied it to multispectral remote sensing thermal images. This newly acquired ability to map different BSC types, using remote sensing, may lead to future applications of habitat and ecological function spatial mapping. We also demonstrate how a fusion of reflective and thermal data can be used to map different land-cover features in a sand dune environment. Our proposed thermal index not only discriminates sand and BSCs, but also enhances the signal from limestone pebbles more than other indices, based on reflective data. Unlike remote sensing in the reflective spectral region, thermal remote sensing is unconstrained by solar illumination. High resolution emissivity signatures of land cover are unaffected by environmental variables, as opposed to land-surface temperature that depends on the time of day and the season.