Abstract: There has been a growing public concern about the impact of the rapid introduction of genetically modified crops (GMCs) on soil ecosystem, especially soil microbial community. In order to verify the effects of decomposition of GMCs straws on soil fungal community structure, classical plate counting and denatured gradient gel electrophoresis (DGGE) were used to analyze cultivable fungi amount and fungal community diversity. Straw of transgenic rice expressing broad-spectrum antifungal proteins was degraded under simulated field conditions. The treatments included soil without straw (S), soil with straws of transgenic rice cultivar of 'Zhuanpin-1' (S-Z1), soil with straws of transgenic rice cultivar of 'Zhuanpin-8' (S-Z8) and soil with straws of non-transgenic rice cultivar of 'Qisiruanzhan' straw (S-CK). The results of traditional culture-dependent method showed significant differences in the amounts of cultivable fungi among transgenic treatments of S-Z1, S-Z8 and non-transgenic treatment of S-CK within 40 days after rice straw decomposition (P < 0.05). However, no significant differences were noted among the above treatments in the period from 40 to 90 days after rice straw decomposition (P > 0.05). The patterns of DGGE of 18S rRNA V1+V2 fragments showed no apparent differences in bands between transgenic and non-transgenic treatments as the different observed bands were largely weak or transient. The positions and lightness of DGGE bands were digitally analyzed using Quantity One software and then the derived Shannon-Wiener index, evenness and abundance to evaluate fungal diversity of different treatments. The results showed significant differences in Shannon-Wiener index and abundance between transgenic and non-transgenic treatments in individual periods of rice straw decomposition such as the first 30 days (P < 0.05). There were no significant differences in evenness between transgenic and non-transgenic treatments during the whole rice straw decomposition period (P > 0.05). Sequence analysis of DGGE-bands showed that most of the bands belonged to Ascomycota, Basidiomycota and Chytridiomycota and the different bands between transgenic and non-transgenic treatments belonged to Ascomycota. The study suggested transient effects of the straw decomposition of transgenic rice expressing broad-spectrum antifungal proteins, but no persistent effects on cultivable fungi count and fungal community structure.