When the soil microbial densities are determined in mangroves and corresponding mudflat at the same tidal level by the dilution plate method, the agar media and dilution water are generally made up of aged seawater in most cases, and effects of salinity in agar media and dilution water on the enumeration of microbes is seldom taken into consideration. The effects of salinity on soil microbial counting from the samples in mangrove areas in Jiulongjiang Estuary of Fujian, and Futian Mangrove Nature Reserve of Shenzhen, China, were tested by dilution plate technique. The results showed that the soil microbial densities in mangroves and mudflat were significantly influenced by the salinity of dilution water and agar media. For the bacteria, the seawater served as sterilized dilution water was significantly (P<0.05) more benefic to the enumeration on the plates than the freshwater, but in reverse for the actinomycetes and fungi. The increasing salinity of media within 35 significantly decreased microbial colonies on the plates, especially for the actinomycetes, in spite of the fact that the effect of salinity of media on fungal numbers was not indefinite. The bacterial colonies were more abundant on the agar plates with low salinity than with high salinity or without any NaCl. It was proposed that some methodological improvements were needed when the dilution plate technique was applied to microbial counting in the samples of mangrove forest and mudflat at the same tidal level in inter-tidal zone. The sterilized dilution water should be prepared with seawater for the bacteria, but with freshwater or low saline water for the actinomycetes and fungi. The salinity of agar media should be low for the microbial isolation and enumeration of soil samples from the mangrove areas including mudflats.