Abstract: Since the parasite infection becomes a focused issue in the research of endangered waterbirds’ conservation, it is urgent to get a simple, rapid and accurate method for parasite examin. The parasite eggs were separated from faecal samples, and treated the eggs by liquid nitrogen / 85℃ water bath, ultrasonication, and cracking fluid digestion, respectively, then detected the different effects using quantitative Realtime PCR. The method used was very well to detect Capillaria by the eggs from Hooded Crane faecals using real-time fluorescence PCR. The results showed cracking fluid digestion had the best effect, this method made the eggs to meet the need of molecular detection by one step pretreatment, providing stable and sensitive detection results with simple and efficient processes. It offered a reliable molecular detection for Capillaria, and also provided a convenient way for detection of the parasitic infection in endangered wild bird species.