An interesting biota of lichen-forming fungi occurs along rocky seashores of cold and warm-temperate regions in both hemispheres. Most of the species belong to the family Verrucariaceae and form symbioses with an extraordinarily diverse group of photobionts. We isolated the photobionts of three species: Hydropunctaria maura and H. amphibia from the supralittoral zone, and Wahlenbergiella striatula from the upper intertidal zone. We characterized the isolated strains structurally by means of transmission electron microscopy, and molecularly using the nrSSU and nrITS and chloroplast RPL10A regions. Additionally, we studied the response of the strains to different salt concentrations, analyzed the concentration of osmoregulatory solutes, and measured photosynthesis performance by chlorophyll fluorescence and CO2 assimilation techniques. All strains belong to the recently described species Halofilum ramosum, although we found differences in the ITS and RPL10A regions among the strains shared by H. maura and H. amphibia and the strain isolated from W. striatula. Differences were also found in the main osmoregulatory response of the strains growing under high salt concentrations: W. striatula accumulated glycerol, while H. maura and H. amphibia synthetized sucrose. Analyses of photosynthesis performance also indicated differences in physiological behavior between supralittoral-dwelling and intertidal-dwelling species, W. striatula showing lower photosynthetic activity under high irradiance. Our results highlight the role of photobionts in determining lichen zonation on rocky seashores.