Many environmental microbes cannot grow in synthesized culture mediums. Therefore, the accuracy of plate count method for the determination of microbial population was low. For fish sauce or similar high salt foods, which usually harbor small microbial populations, it is more difficult to quantify accurately the microbial population using plate count method. The detection of microbial population with real-time fluorescent quantitative PCR (FQ-PCR) method doesn’t rely on cultivation. Therefore, the paper investigated the conditions of the detection of bacterial and fungal populations using FQ-PCR. By comparing the amplification effects of several sets of primers, the bacterial 16S rDNA universal primer 63F-335R and the fungal 18S rDNA universal primer 0817F-1196R were respectively selected as the primers for FQ-PCR detection of bacterial and fungal populations. And the annealing temperatures were determined to be 60 ℃. The selected FQ-PCR primers and the annealing temperatures were validated using many strains of bacteria and fungi. And for any single or mixed strains, the amplification efficiencies were within 90% ~ 120% and the determination coefficients of the standard curves were over 0.98. These results satisfy the requirements of quantification. The bacterial and fungal populations in fish sauce and shrimp sauce were detected by FQ-PCR using the above conditions. The results showed that during the fermentation of fish sauce, the bacterial population varied within the range of 3.16×104- 3.16×105cells/ml, far higher than the fungal population. Besides, the bacterial and fungal populations in fish sauce and shrimp sauce determined by the FQ-PCR method were 1 - 2 orders of magnitude higher than the results determined by plate count method.