Plant roots harbor a large number of fungi that play an important role both in agroecosystems and natural ecosystems. These fungi can be plant pathogenic, parasitic, saprotrophic or mutualistic. The root-associated fungi are involved in various ecological processes in root ecosystems, such as improving plant nutrient uptake, cycling organic carbon, suppressing plant diseases and enhancing plant tolerance to biotic and abiotic stress. In turn, the community and structure of root-associated fungi maybe influenced by rhizosphere conditions such as plant health status, plant growth stage and nutritional status of the plant and soil environments. However, limited information is available about the richness and composition of most of these root-associated fungi as studies of fungal communities remain a challenge because of below-ground high taxonomic and ecological diversity. In the present study, Pisum sativum was used as a model crop to study fungal community structure associated with roots under different environmental conditions. Three individual experiments were conducted in order to study root-associated fungal community structure in relation to root-internal factors in terms of plant health status and plant growth stage and, to a root-external condition in terms of organic fertilization. For identification and semi-quantification of fungal taxa, pyrosequencing combined with DNA barcode technology was applied in this study. Two primer sets (ITS1F/ITS2 and ITS1F/ITS4) from ITS regions were used to generate amplicon reads. Beside the molecular approach, classical fungal identification by microscopy after root staining was also applied. The CLOTU program from the Bioportal package was used for sequence quality control and sequence identification in GenBank. For the statistical analysis, analysis of variance (ANOVA) was used in the measurement of plant growth parameters and relative abundance of root-associated fungi, and principle component analysis (PCA) was used to examine the response of communities of root fungi to the plant and soil environmental factors. vi The three studies showed that root-associated fungal communities were highly diverse and significantly influenced by plant and soil environmental factors, and results supported the hypotheses that the relative abundance of dominant fungal groups differed between healthy and diseased plants, altered according to plant growth stage and responded significantly to different organic fertilizer dosages. In the study of root fungi in relation to plant health status, the richness and abundance of fungal community structures showed clear differences in roots grown in the four soils employed, whereas fungal richness did not correlate with plant health status. A clear succession pattern of rootassociated fungi was formed in pea during the vegetative, flowering and senescence plant growth stages. Pathogenic and arbuscular mycorrhizal (AM) fungi dominated during the vegetative growth stage, whereas saprotrophic fungi dominated during senescence, suggesting that fungal species have different strategies for obtaining organic energy from their host plant. The last study was focused on how soil organic amendments regulated fungal community, generally, the distribution of fungal groups revealed their ecological functional traits; thus obligate biotrophic fungi and saprotrophic fungi were markedly increased with organic fertilizer dosages, while root pathogenic fungi were decreased with organic amendments. In conclusion, the present work has shown that root-associated fungal community structure relate to plant and soil environmental factors. The obtained knowledge from this study can provide novel information of communities of root-associated fungi; thus improving the basic understanding of plant-root fungi-environment interactions in agroecosystems.