Zygophyllum coccineum is a facultative halophyte widely distributed in desert wadis and coastal areas in Egypt. Here, we investigated the influences of maternal habitat on tolerance to salt stress during germination and seedling growth under salinity (0, 100, 200, 400 mM NaCl) of three populations of Z. coccineum from a saline habitat (Manzala coast) and non-saline habitats (Wadi Houf and Wadi Asyuti). In all populations, seed germination started within two days in distilled water but germination indices were reduced significantly with salt level increase. Germination percentage was not significantly greater for seeds from non-saline habitats than for those from the saline habitat under moderate salinity (100, 200 mM NaCl), but only seeds from the saline habitat were able to germinate under high salt stress (400 mM NaCl). Germination recovery was greater for seeds from the saline habitat compared to non-saline populations. At the seedling level, the Manzala population showed the lowest inhibition of shoot length and leaf area under salinity (200 and 400 mM NaCl) compared to non-saline habitats. In the same context, the Manzala population had the maximum chlorophyll a content, superoxide dismutase and esterase activities under salinity compared to non-saline populations, but salinity had a nonsignificant effect on chlorophyll b between the three populations. Carotenoids were enhanced with the increase of salt levels in all populations. These results suggest the salt tolerance of Manzala population is derived from maternal salinity and adaptive plasticity of this species may play an important role in the wide distribution of Z. coccineum.