Rangelands tree species plays a significant role in soil fertility maintenance, providing food, fodder, fuel wood and other uses. However, the impact of tree species on soil properties remains poorly understood. This study evaluates the effect of three dominant indigenous tree species (Acacia melifera, Acacia senegal and Acacia nubica) and one exotic tree species (Prosopis juliflora) with their different sub-habitats on soil physico-chemical properties of Allaidege rangeland, Southern Afar Region of Ethiopia. The results of the study revealed that soil texture (silt and clay), BD, TP, pHe, SOM, TN, CEC and exchangeable bases contents studied were significantly affected (P ≤ 0.05) by tree species of both sub-habitats. Furthermore, the soils textural classes were ranged from silt clay loam to sandy loam in both sub-habitats of tree species. The SOM CEC and TN content were significantly higher soils at indigenous Acacia tree species under canopied sub-habitat than that of Prosopis juliflora under canopied sub-habitat and also higher than uncanopied of all studied tree species. This was more pronounced in the top 20 cm of soil under canopied of Acacia melifera followed by Acacia nubica and senegal tree species, due to better under growth herbaceous layer and also relatively good nitrogen fixing capacity. Therefore, this tree has a significant effect on soil fertility improvement in resource poor rangelands and as a result, it is important to retain scattered indigenous Acacia tree species in Allaidege rangeland.