Arbuscular mycorrhizal fungi are important soil microorganisms belonging to the phylum Glomeromycota, and have a ubiquitous distribution in global terrestrial ecosystems. They are a living bridge for the translocation of nutrients from soil to plant roots and of carbon from plant roots to the soil. Glomalin is a recently discovered glypoproteinaceous substance produced by hyphae and spores of AM fungi that play an important role in structuring soil. Salix psammophila is one of the excellent sand-fixation plants that can not only well stand up to arid desert environment, but also maintain the balance and stability of desert ecosystem. To elucidate the spatial distribution of AM fungi and glomalin and explain the relativity of AM fungi and glomalin with soil factors in rhizosphere of S. psammophila, we sampled from three different sites such as Heichengzi, Zhenglanqi and Yuanshangdu in Inner Mongolia in May 2009. Root samples were taken from four robust S. psammophila, and soil samples from five strata, from ground to deeper layers: 0-10 cm, 10-20 cm, 20-30 cm, 30-40 cm, 40-50 cm, respectively. The results showed that a good symbiotic relation, intermediate type of clumping mycorrhizomata, was formed between AM fungi and S. psammophila; the mean density of AM fungi was 108 spores per 100 g of soil, with a mean of total colonization of 61.7%. There was no significant difference on the total colonization of AM fungi among the three sampling sites (P > 0.05); but the spore densities of AM fungi differed significantly (P < 0.05), with the value at Heichengzi ranking the first. All the highest spore densities were found in the layer of 0-10 cm, and the values decreased with layers deepened. The contents of total extractable glomalin (TEG) and easily extractable glomalin (EEG) were affected by ecological conditions, and also decreased with layers deepened. The means of TEG and EEG were 0.24 and 0.16 mg/g, accounting for 23.6%-24.6% and 14.9%-17.3% of soil organic matter. Both available P and available N in the soil samples showed a negative correlation on spore density (P < 0.05); hyphal colonization was positively correlated with soil organic matter (P < 0.05), but was vesicular colonization negatively done (P < 0.05). Soil phosphatase had a significantly positive correlation with spore density and colonization intensity (P < 0.01). Soil urease was extremely positively correlated with the spore density and colonization (P < 0.01). TEG and EEG were closely related to soil organic matter (P < 0.01). Principal component analysis showed that soil organic matter, phosphatase and available N were the key factors affecting distributions and activities of AM fungi in the desert of Inner Mongolia. The results of the study suggested that glomalin be an appropriate index related to the level of soil fertility, especially in desert areas. Moreover, the paper revealed the relationship among the host plant, AM fungi and the soils, which might be significant to promote vegetative and ecological restoration in deserts.