We studied the influence of added compost, consisting of Acacia cyanophylla leaves, on the production of extra-radical mycelia of arbuscular mycorrhizal (AM) fungi in natural stands of Acacia tortilis, which forms a desert savanna. Four different plots with different soil characteristics in terms of nutrient level and water-holding capacity were included in the study. The production of AM fungi was measured as the increase in the amount of the phospholipid fatty acid (PLFA) 16:1 omega 5 and the neutral lipid fatty acid (NLFA) 16:1 omega 5 in mesh bags placed in the root zone of A. tortilis trees. The production of AM mycelia was much higher at the site with the highest nutrient level and highest water holding capacity. Principal component analysis revealed that mesh bags from this plot had proportionally more PLFA 16:1 omega 5 than the other plots, indicating that this plot contained proportionally more AM fungi in the microbial community. Compost addition enhanced the production of AM mycelia in all plots although the response was greatest in the plot with the highest proportion of AM fungi. The beneficial effect of compost addition on growth of the AM fungal biomass found in this study could be one way to improve survival of planted seedlings in and regions. We suggest that indigenous AM fungi, which are adapted to the limiting conditions in the plots, are the preferable source of inoculum for improving the growth of A. tortilis in plantations in pre-Saharan ecosystems.