Calcium cyanamide (CaCN(2)) has been one of the potential candidates as soil disinfectant since the restriction of methyl bromide in soil fumigation due to its ecological risk. However, little information is available on effects of CaCN(2) on soil microbial community. In this study, the soil microbial communities and the fate of pathogen Fusarium oxysporum (Schlechtend, Fr) f. sp. cucumberinum (Owen) Snyder and Hansen (F.O. f. sp. cucumberinum) in response to CaCN(2) treatment was evaluated. F.O. f. sp. cucumberinum population in soil treated with CaCN(2) at rates of 80 and 200 gm(-2) was suppressed by 88.7 and 92.2% after 15 d of CaCN(2) application. Bacterial, fungal, and actinomycete populations were also greatly decreased after 3 d of CaCN(2) application, but they recovered to the control level by 15 d. The variation in functional diversity of soil microbes characterized by principal component analysis, diversity and evenness indices based on Biolog data followed a similar trend. Meanwhile, the band number from the DGGE of soil 16S rDNA fragments increased from 9 for the non-CaCN(2)-treated soil to 10 or 12 after different rates of CaCN(2) application at 15 d, indicating the increase of abundant rDNA types in the community. The results suggest that CaCN(2) application had only a short-term and transitory impact on the indigenous soil microbial community in contrast to the long-term suppression of the F.O. f. sp. cucumberinum population. It is feasible to reduce Fusarium wilt without significant impact on microbial community by application of CaCN(2) at reasonable doses.