本研究在探討臺灣四種蘭科植物（Orchidaceae）根部之微生物菌相。採自短穗斑葉蘭、馬鞭蘭、臺灣春蘭及竹柏蘭根部所分離得真菌39株與細菌35株，以脂肪酸甲酯鑑定系統及分子鑑定之序列分析作為分類依據，並使用Neighbor-joining method （NJ）、Maximum parsimony method （MP）和MrBayes method （MB）三種方法作親緣關係之分析。實驗結果發現不同蘭科植物之真菌族群具差異性，優勢菌株隨寄主有所變化，Trichoderma spp.和Cladosporium spp.，皆普遍存在於蘭科植物根部中；細菌族群是以Pseudomonas spp.、Bacillus spp.為主，皆存在於四種蘭科植物根部中。利用Neighbor-joining method （NJ）、Maximum parsimony method （MP）和MrBayes method （MB）三種親緣關係之分析方法對真菌與細菌之序列進行分析，所得之結果與傳統形態之鑑定結果大致相同，顯示以此分析可作為真菌和細菌微生物物種分類之可靠方法。

　Orchidaceae is one of the largest families in the plant kingdom. Orchids require a symbiotic relationship with fungi for germination and seeding nutrition. These kinds of symbiotic fungi are called “orchid mycorrhizal fungi” or “orchid fungi”. This study is to confer the microflora isolated from the roots of Taiwan native Orchidaceae. Thirty-nine strains of fungi and 35 strains of bacteria were isolated from Goodyera maximowicziana Makino, Cremastra appendiculata (D. Don) Makino, Cymbidium formosanum Hayata var. formosanum and Cymbidium lacifolium Hook. f. var. lancifolium. The strains were analyzed and classed by the fatty acid methyl ester (FAME) and the molecular methods, ITS and 16S ribosomal DNA were chosen as the target DNA. Their phylogenetic relationship were examined by NJ, MP and MB methods. The result of this study showed that, the fungi flora was diverged, the dominant strains were changed by various. The fungi of Trichoderma spp. and Cladosporium spp. and the bacteria of Bacillus spp. and Pseudomonas spp. were widespread existed in the roots of orchids. The phylogenetic relationship obtained by NJ, MP and MB methods were approximately the same as the traditional morphological classification. It showed that the molecular analysis can be a useful tool for the rapid identification of roots associated fungi and bacteria.