Reproductive strategies for specific populations are closely related to environmental factors. Consequently, they are fundamental for conservation plans and the management of threatened habitats like salt marshes. From this viewpoint, germination strategy under different temperatures and salt conditions, voltammetric parameters and molecular analysis were performed and compared in six Halocnemum populations (four of H. cruciatum and two of H. strobilaceum) growing on Mediterranean (Balearic, Tyrrenic and Adriatic) and Red Sea coasts to establish the relation to environmental variables. Significant interpopulation differences were found in all the evaluated parameters. The Mediterranean populations showed a variable opportunistic germination strategy that was directly related to the drought period length at the studied sites. Consequently, potential environmental predictors of seed response were identified. The most noteworthy were bioclimate, soil texture, continentality index, winter temperatures and summer precipitations. Additionally, voltammetric parameters were evidenced as indicators of maternal plant stress levels and, thus, as potential determinants of future seed responses. The phylogenetic analyses showed a split into two species that did not correspond to germination response. The phylogeographic analyses showed interpopulation differences in haplotype composition for H. cruciatum, but not for H. strobilaceum. In conclusion, the tight connection between seed responses and the ecological parameters of natural populations as an adaptation for successful seedling emergence was proved regardless of its phylogenetic relations.