Organic fertilization is well known to affect individual functional groups of root associated fungi such as arbuscular mycorrhizal (AM) fungi and root pathogens, but limited information is available on the effect of organic fertilization at the fungal community composition level. The main objective of the present study was to examine the response of communities of root associated fungi in Pisum sativum to Protamylasse, an organic fertilizer used in pea production. Plants were grown in pots with field soil amended with four different levels of Protamylasse. 454 pyrosequencing was employed to examine diversity of root associated fungi and revealed in total 164 non-singleton operational taxonomic units (OTUs). Principle component analysis (PCA) showed response of fungal community structure of the 15 most abundant OTUs to the four fertilization levels. Obligate biotrophic fungi such as the AM fungi Glomus mosseae and Glomus caledonium, and the chytridiomycete Olpidium brassicae markedly increased in relative abundance with increasing levels of Protamylasse, whereas the relative abundance of the facultative pathogen Fusarium oxysporum decreased with increasing levels of Protamylasse. In conclusion, the organic fertilizer Protamylasse clearly affects communities of root associated fungi, which seems to be linked to the life strategy of the different functional groups of root associated fungi.