Soil salinity is a significant environmental stressor that impacts species distribution, plant development, and genetic diversity. Conservation and ecological management depend on an understanding of how Tetraena species respond to salinity. The genus Tetraena, which includes several species of succulent shrubs native to arid regions, is of significant interest for studying plant adaptation mechanisms. The study aims to evaluate the genetic diversity and ecological characteristics of eight groups of Tetraena species in Saudi Arabia using inter-retrotransposon amplified polymorphism (IRAP) markers, ycf5 and trnH gene sequences, as well as soil pH and electrical conductivity (EC). Soil pH indicated slightly alkaline conditions, while electrical conductivity (EC) ranged from 822 μS/cm in the T. propinqua population at Al Thumama Road (population 8) to 23,800 μS/cm in the T. hamiensis population at Al Jawhara-Dammam Road (population 2). The genetic relationships were determined by analyzing IRAP marker polymorphism, generated using 10 primers. Clustering through principal component analysis and biostatistical methods distinguished the populations of T. propinqua subsp. Migahidii (6, 7, and 8) from the populations of T. hamiensis var. qatarensis (1, 3), (4, 5), and (2). Ten primers had high polymorphism (60.5%) according to IRAP analysis between T. hamiensis and T. propinqua. The evolutionary trees of T. propinqua and T. hamiensis cluster together. Analysis of conserved motifs revealed common motifs that support the use of ycf5 and trnH as barcodes. The genetic diversity and population clustering of T. hamiensis and T. propinqua are influenced by environmental salinity and species-specific genetic adaptations. While T. hamiensis has more differentiation, maybe as a result of historical separation or localized adaptations, T. propinqua exhibits strong genetic similarities. These results demonstrate that common environmental stresses and species-specific characteristics are the main drivers of genetic diversity. Future studies should explore adaptive genetic mechanisms at the molecular level and assess the functional roles of salinity-responsive genes in support conservation efforts.