破囊壺菌 (Thraustochytrium) 為一群絕對海生的雙鞭毛真菌，生活在半鹹海水中，以腐生或寄生方式在有機物上休眠和著生，在河口的碎食性食物鏈扮演分解者角色；一般只能利用誘釣的方式加以分離培養，並無法直接觀察其在自然環境中所利用的基質類別，本研究嘗試使用定性及定量方法篩選純種保存的破囊壺菌各菌株的蛋白質分解 (protease) 活性。結果顯示有7種16個菌株可以分解利用蛋白質，其中分離自四草生態保護區沼澤底泥的二株多增殖性破囊壺菌 (T. multirudimentale) 比其他分離自水體中的菌株具有較強的蛋白質分解能力；佐證可資利用的生物性基質種類也是影響鞭毛菌種類消長與分佈的因素之一。 The obligate marine, biflagellatic Thraustochytrids are saprotrophic or paratrophic on algal and vascular plant materials and play the decomposers in marine foodchain. They also have been isolated from the guts of echinoderms and from sponges, but the nature of associations is unknown. However only rarely have been observed in nature. Most of them has come from laboratory studies of species isolated using pollen grains as bait in water and sediment samples. This project is to investigate the protease activity of pure cultured Thraustocytrids. The qualitative analysis reveals 7 species 16 strains with the ability to utilize protein. The quantitative analysis shows two strains of T. multirudimentale with the notablest of protease activity. They are isolated from the sediment in protected area of Sze-Tsao. This reveals the substrate is one of the factors that effects the scattering of Thraustochytrids.