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The occurrence of arbuscular mycorrhizal fungi (AMF) was assessed by both morphological and molecular criteria in two salt marshes: (i) a NaCl site of the island Terschelling, Atlantic Coast, the Netherlands and (ii) a K2CO3 marsh at Schreyahn, Northern Germany. The overall biodiversity of AMF, based on sequence analysis, was comparably low in roots at both sites. However, the morphological spore analyses from soil samples of both sites exhibited a higher AMF biodiversity.Glomus geosporumwas the only fungus of theGlomeralesthat was detected both as spores in soil samples and in roots of the AMF-colonized salt plantsAster tripoliumandPuccinelliasp. at both saline sites and on all sampling dates (one exception). In roots, sequences ofGlomus intraradicesprevailed, but this fungus could not be identified unambiguously from DNA of soil spores. Likewise,Glomussp. uncultured, only deposited as sequence in the database, was widely detected by DNA sequencing in root samples. All attempts to obtain the corresponding sequences from spores isolated from soil samples failed consistently. A small sizedArchaeosporasp. was detected, either/or by morphological and molecular analyses, in roots or soil spores, in dead AMF spores or orobatid mites. The study noted inconsistencies between morphological characterization and identification by DNA sequencing of the 5.8S rDNA-ITS2 region or part of the 18S rDNA gene. The distribution of AMF unlikely followed the salt gradient at both sites, in contrast to the zone formation of plant species. Zygotes of the algaVaucheria erythrospora(Xanthophyceae) were retrieved and should not be misidentified with AMF spores.