<p>Halophytes host diverse fungal communities that can influence plant fitness and whole ecosystem functioning. Despite their importance, general knowledge on the root-associated endophytic fungal microbiomes of halophytes is limited to few species. In our study, we investigated fungal microbiomes associated with roots of two annual (<i>Salicornia procumbens</i> and <i>Suaeda maritima</i>, both Amaranthaceae) and two perennial (<i>Atriplex portulacoides</i>, Amaranthaceae, and <i>Puccinellia maritima</i>, Poaceae) halophytes using amplicon sequencing of nuclear ribosomal DNA. We investigated the fungal communities with respect to host life history strategy, host identity and seasonality. Moreover, we investigated species-specific root anatomical traits, which could potentially influence microbiome assembly. Overall, our results revealed a strong effect of host identity on fungal microbiomes. Furthermore, variation in microbiome composition throughout seasons seems to be a species-specific process which does not depend on plant life history strategy. We observed higher richness, diversity and evenness in samples of the grass <i>P. maritima</i> compared to the three Amaranthaceae, particularly those collected in autumn. Species-specific root anatomical traits, such as larger roots cells in <i>P. maritima</i> go along with the higher diversity. The fungal orders Pleosporales and Xylariales were, in general, the most common endophytes in all species, but Glomeromycota was also detected in roots of <i>P. maritima</i> in summer. Overall, our study provides a better understanding on the dynamics of fungal microbiome assembly in roots of halophytes throughout seasons emphasizing the importance of host identity on fungal microbiome assembly.</p>