The analytical method for the determination of methylmercury in seabird excrements was established using atomic fluorescence spectrometry coupled with microwave-assisted extraction. In general, temperature and hydrochloric amount are the most important influencing factors on the extraction of MeHg in the samples, and the present paper optimized these two parameters. The result showed that 120 ℃ and 200 μL 6 mol·L-1 hydrochloric acid are the best extraction conditions. Under these experimental conditions, the relative standard deviation (RSD) values of reduplicative analyses on standard reference material (human hair powder) and the same seabird excrement sample were 0.74% and 6.61% respectively, and their percent recoveries were over 90%. The combination of microwave-assisted extraction and atomic fluorescence spectrometry has many advantages such as simple operation, high sensitivity, low detection limit and low cost, therefore, it is suitable for rapid separation and analysis of trace methylmercury composition in the biological guanos. Using this method, we analyzed the methylmercury contents in the ancient and fresh seabird droppings taken from Xisha Islands of South China Sea, and the result showed that the Xisha guanos were rich in methylmercury and the large input of seabird guanos will cause serious environmental contamination in the remote island ecosystem of Xisha Islands.