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Functional diversity in ecosystems has traditionally been studied using aboveground plant traits. Despite the known effect of plant traits on the microbial community composition, their effects on the microbial functional diversity are only starting to be assessed. In this study, the phylogenetic structure of arbuscular mycorrhizal (AM) fungal communities associated with plant species differing in life cycle and growth form, that is, plant life forms, was determined to unravel the effect of plant traits on the functional diversity of this fungal group. The results of the 454 pyrosequencing showed that the AM fungal community composition differed across plant life forms and this effect was dependent on the soil collection date. Plants with ruderal characteristics tended to associate with phylogenetically clustered AM fungal communities. By contrast, plants with resource-conservative traits associated with phylogenetically overdispersed AM fungal communities. Additionally, the soil collected in different seasons yielded AM fungal communities with different phylogenetic dispersion. In summary, we found that the phylogenetic structure, and hence the functional diversity, of AM fungal communities is dependent on plant traits. This finding adds value to the use of plant traits for the evaluation of belowground ecosystem diversity, functions and processes. ; We thank Dr. Rasmus Kjøller and two anonymous reviewers for valuable comments on the manuscript, and Dr. Francisco Bruno Navarro, Domingo Álvarez and Estefanía Berrio for assistance during experiment set‐up and analysis. Funding was provided by Spanish Plan Nacional de I + D + I (project CGL‐2009‐08825) and the Junta de Andalucía, Consejería de Economía, Innovación y Ciencia (project CVI‐7640). SVC and ALG were supported by the Formación de Personal Investigador Programme (Ministerio de Ciencia e Innovación, Spain). During manuscript preparation, ALG was supported by the European Commission under the European Union's Horizon 2020 research and innovation programme (Marie Curie Individual Fellowship grant agreement no. 708530). MO and MV were supported by Estonian Research Council (grant IUT20‐28) and European Regional Development Fund (Centre of Excellence EcolChange). We also thank Consejería de Medio Ambiente, Junta de Andalucía, for permission to work in the Sierra de Baza Natural Park as well as the Real Jardín Botánico (CSIC) and the Banco de Germoplasma Vegetal Andaluz (Junta de Andalucía) for providing us with the seeds used in this study. ; Peer Reviewed