Macroarray and Real-time quantitative polymerase chain reaction (Real-time PCR) methods were used to perform quick check and quick quantification of Fusarium oxysporum in soils infected with watermelon wilt disease, and their usage was optimized and studied in lab. Results show that in rhizospheric soils of Treatments N^-+ P^-and N^-+ P⁺ severely infected with the disease, the Macroarray System detected strong positive signals, indicating that Fusarium oxysporum existed in these soils in large quantity. The real-time PCR method also found that the number of Fusarium oxysporum in treatments N^-+P^- and N^-+ P⁺ was the largest, being up to 8.89×10⁵ dRn g^-1 soil and 2.24×10⁵dRn g^- soil, respectively, while in other two treatments not infected with the disease, the number was 6.23×10³dRn g^-soil and 3.28×10³ dRn g^-1soil. While in bulk soils of all the four treatments, the number of Fusarium oxysporum varied between 10²~10³ dRn g^-1 soil, and the Macroarray System didn’t detect any strong positive signals. Compared to the traditional isolation, culture, plate screening and counting method for identification and detection of pathogens, the two above described methods are accurate, instant, and time-and-labor saving.