本研究是以粒線體DNA之COI核酸序列當作分子遺傳標記，共分析台灣地區淡水產哲水蚤（Calanoida）右突新鏢水蚤 Neodiaptomus schmackeri 四個族群51個樣本，錐肢蒙鏢水蚤Mongolodiaptomus birulai 五個族群65個樣本，定序結果獲得右突新鏢水蚤Neodiaptomus schmackeri 635bp的序列長度，錐肢蒙鏢水蚤Mongolodiaptomus birulai 655bp的序列長度，分別得到8種及14種單套基因型（Haplotype）。以族群間分化指數（Fst）及基因交流指數（Nm）分析，除台南曾文水庫及烏山頭水庫的錐肢蒙鏢水蚤Mongolodiaptomus birulai彼此基因交流暢通外（Fst=0.058； Nm=4.04），其餘族群間基因交流皆不順暢（Fst：0.4~0.99； Nm：0~0.37），顯示族群分化程度明顯，隔離效應顯著。
以近鄰歸群法（neighbor-joining method）分析所得之地理親緣關係樹（Geophylogenetic tree），其結果皆顯示新竹寶山水庫之族群與其他地區族群分歧較大，成為一獨立之類群，分支可信度為99%。同時，各地的族群皆各自成一類群未有相互混雜之情形，分化程度明顯但未符合距離隔離模式，各地族群大致會聚集在一起，唯一例外的是錐肢蒙鏢水蚤Mongolodiaptomus birulai中的曾文水庫與烏山頭水庫個體在圖形上會呈現鑲嵌狀，且有些基因型會同時出現在兩地，而無明顯的分化現象。

I use the mtDNA COI ( Cytochrome Oxidase I )sequence as genetic maker to analysis the population genetic structure of two species freshwater copepod, Neodiaptomus schmackeri and Mongolodiaptomus birulai (Calanoida:copepoda) in Taiwan.　I have four populations, 51 individuals of N. schmackeri, and five populations, 65 individuals of M. birulai. I compared nucleotide sequences of a 635 bp fragment from the COI gene of N. schmackeri, 8 unique haplotypes were recorded ; 655 bp fragment from the COI gene of M. birulai, 14 unique haplotypes were recorded. Except the gene flow between the Tseng-wen reservoir and Wu-sa-nto reservoir was umlimted (Fst=0.058； Nm=4.04), the gene flow of all the other populations are limited (Fst：0.4~0.99； Nm：0~0.37).　Based on the COI gene diversification data, I suggest
that the most population of N. schmackeri and M. birulai are isolated. The Geophylogenetic relationships are inferred by the neighbor-joining method. In the M. birulai, all the individuals are grouped in the right place of collecting site, but the Tseng-wen reservoir and Wu-sa-nto reservoir are grouped together.　In the N. schmackeri, all the individuals are grouped in the right place of collecting site, the most dived population is N. schmackeri of Bao-shan reservoir with confidence of 99%.　Genetic distance was not correlated with geographic distance, the genetic diversification pattern is not comparable to higher isolation of longer distance separation.

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