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Abstract The Southeastern Anatolian Project (SAP, Turkish acronym GAP) is the largest irrigation and development project of Turkey covering about two million ha cultivated land. A number of field experiments in the region with different crops including maize, wheat, and cotton, have repeatedly shown that increased applications of phosphorus (P) fertilizers (i.e., from 0 kg P2O5 ha−1 up to 200 kg P2O5 ha−1) do not lead to any effects on crop yield in soils with low plant available P concentration. The aim of the research was to determine the potential effect of indigenous mycorrhiza and selected mycorrhiza species on plant growth and nutrient uptake under sterile and non‐sterile soil conditions. The preliminary results led us to study the effect of indigenous mycorrhizae potential on the growth of plants and P nutrition in a representative soil from the GAP under greenhouse conditions. Using inoculation of three different mycorrhizae species (Glomus caledonium, G. etunicatum, and G. mossea) maize plants were grown with increasing P [0 (P1), 25 (P2), 125 (P3) mg P kg−1 soil] supply in soils with and without sterilization. At the lowest P supply, shoot dry matter production was significantly depressed. This decreasing effect of low P supply was particularly obvious when soils were sterilized and not inoculated with mycorrhizae. Inoculation of soil with mycorrhizae species significantly increased plant growth and P uptake of plants, especially under low P supply and soil sterilization. In all experiments, plants grown on non‐sterile soil grew much better than on sterilized soils. However, mycorrhizal dependencies of plant grow in sterile soil is higher than that in non‐sterile soil. Among the mycorrhizae species, G. caledonium was the most effective on plant growth, P uptake and mycorrhizal dependency. In low P application, plant roots were strongly infected and consequently increased plant growth, but in high P level application there was a slight reduction in root infection. The results show that mycorrhizal inoculation is an effective practice for improving crop production in P deficient soils. Also there was a potential effect of indigenous mycorrhizal fungi spores in the soil series of the Harran Plain that successfully infected the plant roots. It has been concluded that soil and crop management can help to get maximum benefit from indigenous mycorrhiza for sustainable P management.