Mesquite (Prosopis juliflora) is an invasive plant that is threatening agricultural lands and native floral diversity because of its ability to adapt and grow rapidly under environmental conditions of arid and semi-arid areas, urging the Omani government to launch the national campaign for mesquite eradication in 2016. Its invasion appears to be driven by allelopathy, a biological phenomenon by which P. juliflora releases allelochemicals influencing the neighboring plants negatively. However, little is known about the effects of the invasive species on the vegetation cover especially indigenous trees at realistic concentrations of its allelochemicals. Furthermore, the plants exposed to the allelochemicals extracted from different parts of P. juliflora show variable responses with limited understanding on how these allelochemicals interfere with molecular components of the target plants. Here, we aim to study and determine the allelopathic effects of P. juliflora on two common Omani plant species (the native ghaf, Prosopis cineraria, and samr or acacia tree, Vachellia tortilis) using water or aqueous extracts and powders of P. juliflora leaves and pods. Seeds of P. cineraria and V. tortilis were exposed to low levels (compared to previous investigations) of leaves/pods powders (0.5 and 5.0% w/w) or concentrations of their aqueous extracts (10 and 100 mg/L), planted in 1:1 mixed media (sandy soil: compost), and seedlings were observed for 28 days after germination. Seed germination percentages as well as growth parameters (length of root and fresh mass of seedlings of both species) were not significantly affected by the presence of aqueous extracts or powders of P. juliflora leaves and pods. While the exposed V. tortilis seedlings had higher content of chlorophylls a and b particularly with treatment of pod extracts and powders, no change in these pigments was observed for P. cineraria seedlings. On the contrary, there was an increase in the content of carotenoids in P. cineraria seedlings exposed to the extracts and reduction in the content for the seedlings exposed to the powders. Neither P. juliflora extracts nor powders influenced carotenoids content of V. tortilis seedlings. Unlike the V. tortilis seedlings, exposure to P. juliflora powders resulted in higher accumulation of proline in the P. cineraria seedlings, indicating a stressful condition imposed by the invasive species. The relatively low levels of allelochemicals may not impede processes (e.g. mitotic division) responsible for root elongation and shoot development of the studied plants. Despite the inconsistent responses observed for leaves and pods extracts and powders, the measured effects appeared to be more pronounced in presence of the powders compared to water extracts of P. juliflora. Our laboratory-based experiments generally revealed limited allelopathic effects of the invasive species on native plants (P. cineraria and V. tortilis), nevertheless further studies should be carried out in field soils sampled near or under the canopy of P. juliflora due to accumulation of leaves that may be somewhat affecting neighboring plants.