在台南沿海地區選定曾文溪河口、沿海養殖魚塭、魚塭間引水道、及公路旁水渠四種樣區，進行海生鞭毛真菌相調查，並分析其多樣性與環境因子的關係。研究期間共分離50株海生鞭毛真菌，經鑑定為3屬14種，包括：破囊壺菌(Thraustochytrium)11種、裂殖壺菌屬(Schizochytrium)2種以及吾肯氏壺菌屬(Ulkenia)1種。四個樣區以魚塭的種豐富度(S＝9)最高，三次採樣以一月份的種豐富度(S＝10)最高，四月份(S＝4)最低；U. minuta、T. motivum及T. aggregatum在四個採樣點都出現，其中T. motivum出現頻率(Pi＝11/50)最高，可視為此地區的優勢種；魚池引水道與公路旁水渠兩個樣區之間相似度(PS＝66.67)最高。影響鞭毛真菌種類數的最適環境因子分別是：水溫15-20℃、鹽度3-4.4%、約pH 8.1的水質。 Thraustochytrids are common microfungi in marine water, but their distribution and diversity in southwestern coastwise are poorly described. In this study we investigated the distribution and diversity of thraustochytrids in marine water which were collected from estuary, fishpond, diverted waterways among fishponds, and ditches beside highways. Fifty strains of marine Mastigomycotina were isolated and identified as fourteen species in three genus, eleven species of Thraustochytrium, two species of Schizochytrium, and one species of Ulkenia. The most of thraustochytrid species (S = 9) was isolated from fishpond. The most of thraustochytrid species (S = 10) was observed in January, and the least (S = 4) occurred in April. T. motivum was the ubiquitous and dominant species (Pi = 11/50). The similarity (PS = 66.67) was high between diverted waterways among fishponds and ditches beside highways. Water temperature 15-20℃, salinity 3-4.4 % and about pH 8.1 were optimal factors for the Mastigomycotina species.