Abstract: Fungi are critical for the decomposition of terrestrial organic matter and subsequent global carbon cycle. High microbial diversity is essential for efficient nutrient recycling in soils. To investigate the impacts of different application modes of fertilizers on fungal communities, a long-term fertilization experiment (of over 20 years of continuous fertilizer treatments) was conducted in North China. Soil samples were collected from 4 treatments: effective microorganisms compost (EM), traditional compost (OF), chemical fertilizer (CF) and unfertilized control (CK) from March to October in 2012. The T-RFLP analysis, which is a polymerase chain reaction (PCR)-fingerprinting method commonly used for comparative microbial community analysis, was used to analyze the soil samples. Because of differences in T-RFLP patterns, a series of analyses - diversity index analysis, principal component analysis (PCA) and redundancy analysis (RDA) - was used to further determine soil fungal diversity in different treatments. Several multi-variate statistical approaches were used to interpret and compare the changes in T-RFLP fingerprints derived from different communities. Then the principal component analysis (PCA) and redundancy analysis (RDA) were particularly used in determining the trends in T-RFLP data. The results showed that fungal community structures in EM and OF were different from those in CK and CF. The ranges of Shannon-Weiner diversity index and the Simpson index in the samples were 2.64-3.53 and 0.03-0.08, respectively, under fertilzation treatments. While the highest Shannon-Weiner diversity index was in October and at the 0-20 cm soil layer under OF and EM treatments, the lowest was in March and at the 0-20 cm soil layer under CK treatment. Also while the highest Simpson index was in March and at the 0-20 cm soil layer under CK treatment, the lowest was in October and at the 0-20 cm soil layer under OF and EM treatments. Based on the comprehensive evaluation indexes of fungal community using PCA of T-RFs peak area and Shannon-Weiner index, fungal community was higher in EM and OF than in CF and CK treatments. The high fungal diversities in EM and OF treatments occurred in March, June and October. PCA analysis indicated that soil fungi under EM, OF, CF and CK treatments formed independent community structures. The communities were adaptable to own specific soil environments to form the dominant population. Redundancy analysis showed that fungal community composition was significantly influenced by soil pH, organic matter, total nitrogen, available phosphorus and available potassium. The above findings contributed significantly to the understanding of the specific changes in soil fungal diversity and fungal community in response to different fertilization treatments. The addition of different organic fertilizers improved a range of soil properties related with microbial activities after 19 years of treatment. Also fungi community became more diverse after application of organic fertilizer. It was concluded that organic fertilizer application was best strategy for increasing diversity of soil fungi.