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—The mesquite tree (Prosopis laevigata), besides its conventional uses, has a high potential to recover agricultural areas with salinity problems. It improves the physical and chemical properties of the soil, and in the rehabilitation of degraded arid and semi-arid zones, or those tending to desertification.The aim of this research was to test the effect of organic fertilization and inoculation withGlomus sp. on mesquite trees. We did the experiment under greenhouse conditions. The effect of applying Glomus sp. and organic matter in different doses during the growth of shoots and roots was evaluated in 13 agronomic variables in mesquite seedlings grown in Lithosols and Xerosols soils. We used a complete randomized block design with three replications. After 180 days, we analyzed the data using Statistical Analysis Software (SAS) version 9.2. We observed a positive and significant effect on the growth of the agronomic variables studied under greenhouse conditions, and inoculation with Glomus sp. The organic matter factor presented significant differences (p ≤ 0.05). We determined that the ideal dose was 55 g per experimental unit. According to the soil used, positive effects (p ≤ 0.05) were observed for 50% of the agronomic variables in the Xerosols soil with relation to the Lithosols soil.We concluded that the inoculation of Prosopis laevigata with Glomussp., and adding organic matter favors the growth of both the shots and the roots of the plant.