Arbuscular mycorrhizal (AM) fungi often colonize the roots of mangrove plants, forming symbiotic associations with them, but colonization rates differ greatly among mangrove species. To examine differences in the colonization patterns of AM fungi, we focused on two species of mangroves (Rhizophora stylosa and Bruguiera gymnorhiza; Rhizophoraceae) and conducted a pot experiment using seedlings grown in mangrove soil watered with fresh water or brackish water (200 mM NaCl). We observed AM fungal structures such as hyphae, arbuscles, and vesicles in the roots of all B. gymnorhiza seedlings in the freshwater treatment, but rarely in the brackish water treatment. By contrast, we found no AM fungal structures in roots of any R. stylosa seedlings in either the freshwater or brackish water treatment. These results imply that B. gymnorhiza are facultatively mycorrhizal plants that have maintained the ability to form associations with AM fungi, whereas R. stylosa, which dominate habitats more seaward than those of B. gymnorhiza, may have lost the ability to form mycorrhizal associations through adaptation to extreme seaside conditions.