Salt stress is one of the most common abiotic kinds of stress. Understanding the key mechanisms of salt tolerance in plants involves the study of halophytes. The effect of salinity was studied in two halophytic annuals of Chenopodiaceae Salicornia perennans Willd. and Climacoptera crassa (Bied.) Botsch. These species are plants with C3 and C4-metabolism, respectively. We performed a comprehensive analysis of the photosynthetic apparatus of these halophyte species at different levels of integration. The C3 species S. perennans showed larger variation in leaf functional traits—both at the level of cell morphology and membrane system (chloroplast envelope and thylakoid). S. perennans also had larger photosynthetic cells, by 10–15 times, and more effective mechanisms of osmoregulation and protecting cells against the toxic effect of Na+. Salinity caused changes in photosynthetic tissues of C. crassa such as an increase of the mesophyll cell surface, the expansion of the interface area between mesophyll and bundle sheath cells, and an increase of the volume of the latter. These functional changes compensated for scarce CO2 supply when salinity increased. Overall, we concluded that these C3 and C4 Chenopodiaceae species demonstrated different responses to salinity, both at the cellular and subcellular levels.