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臺灣光復後魚類學的研究也是從分類開始，確認魚類的種名是從事魚類生態、生物學 (年齡成長、食性、生殖成熟、生理、行為)、生活史、洄游、演化、保育及資源永續利用的第一步。學術文章要發表也得要先確定魚種的學名，才能夠做到科學最重要的條件，可重現性以及可比較性。
陳兼善教授是臺灣最早魚類分類研究的推手，他在1956年出版的《臺灣脊椎動物誌》中，共記錄870種魚類，被用作大學魚類分類學的課本長達40年之久。梁潤生及沈世傑教授算是第二代。沈教授自1967起在國立臺灣大學動物系講授魚類分類學亦長達40年。他1993年主編的《臺灣魚類誌》共整理出2,028種。上過沈老師課的學生算是第三代，包括莫顯蕎及邵廣昭專攻海水魚類，曾晴賢則專攻淡水魚類，後來他們都拓展到生態、演化和保育等不同的領域；畢業於日本東京大學的國立臺灣海洋大學的陳哲聰教授則專攻軟骨魚類分類及漁業生物學。
2000年後第三代老師們所指導的碩博士生，如陳餘鋆、王弘毅、莊守正、陳正平、陳義雄、陳鴻鳴、何宣慶、廖運志、李茂熒、邱詠傑等算是第四代，他們所指導的學生們則是第五代。他們除了利用傳統形態之外，也利用DNA或生命條碼作了許多目、科或屬的系統分類學的研究，包括分類整理及探討類緣關係等。前後共發表了至少400種以上的世界新種及上千種的臺灣新紀錄種，成果豐碩，真可謂是長江後浪推前浪，江山代有人才出。
另外，還有幾位從海外直接學成回國表現傑出的學者，如陳韋仁、廖德裕、林秀瑾等在分子親緣關係的探討，林千翔應用耳石或其化石在魚類分類及重建古生物多樣性及生物地理學方面的研究。臺灣在魚類分類學研究的實力堅強，這與臺灣優越的地理位置以及豐富的魚類多樣性有直接的關聯。除了成魚的分類外，在魚卵和仔稚魚方面，利用生命條碼鑑種的方法也有很好的成績。臺灣魚類資料庫的建置迄今也有35年的歷史，在國內外頗受歡迎及好評。故臺灣能在2005年及2025年爭取到在台北主辦第7屆和第12屆的印度太平洋魚類會議，也為臺灣帶來許多魚類研究的契機。
本文的內容除了介紹上述從事臺灣魚類分類學研究的主要學者及其在分類上的貢獻之外，亦就魚類分類系統的演進、臺灣標本典藏的狀況、資料庫中魚種數的統計、臺灣魚類地理分布的類型及其形成的機制、魚卵及仔稚魚的分類、海峽兩岸魚類研究的合作交流，以及魚類分類研究的困難及展望等分別作扼要的整理，希能為臺灣魚類分類研究留下歷史性的紀錄。

摘要abstract(英) The study of the taxonomy of Taiwanese fishes started as early as 1858. Europeans, Canadians, and Americans were the pioneers in studying the fish fauna of Taiwan. After the Sino-Japanese war (1894–1895), China ceded Taiwan to Japan, and Japanese zoologists started the taxonomic study of Taiwanese fishes. After the end of WWII, Japan ended its colonial rule (1895–1945), and ichthyologists in Taiwan started their own studies on fish classification. Professor Johnson Ta-Fu Chen was the earliest pioneer of fish taxonomy research in Taiwan. In 1954, he published the first edition of Fishes of Taiwan, which included 140 families and 675 species of fishes, along with key to all species. His A synopsis of the vertebrates of Taiwan, published in 1956, recorded a total of 870 species of fish and was used as a textbook on fish taxonomy in universities for more than 40 years. Professors Ren-Sheng Liang and Shih-Chieh Shen are considered the second generation of ichthyologists. Prof. Shen has been teaching fish taxonomy at the Department of Zoology, National Taiwan University, for more than 40 years since 1967. The Fishes of Taiwan he edited in 1993 compiled a total of 2,028 species. Students who took Prof. Shen's classes are considered the third generation, including Hin-Kiu Mok and Kwang-Tsao Shao, who specialized in marine fishes, and Chyng-Shyan Tzeng, who specialized in freshwater fishes. Later, they expanded into different fields such as ecology, evolution, and conservation. Prof. Che-Tsung Chen of National Taiwan Ocean University, a graduate of the University of Tokyo, specialized in cartilaginous fishes and fishery biology. The master's or doctoral students supervised by the third generation after 2000, including Yu-Yun Chen, Hurng-Yi Wang, Shoou-Jeng Joung, Jeng-Ping Chen, I-Shiung Chen, Hong-Ming Chen, Hsuan-Ching Ho, Yun-Chih Liao, and Mao-Ying Lee, are considered the fourth generation, while the students supervised by them represent the fifth generation. In addition to using traditional morphological study methods, they also integrated genetics or DNA barcoding to conduct taxonomic or phylogenetic studies across various taxa, including species classification and exploration of their phylogeny. More than 400 new species and 1,000 new records in Taiwan have been described or documented. The results have been fruitful. In addition, several outstanding scholars returned to Taiwan directly after studying abroad, including Wei-Jen Chen, Te-Yu Liao, and Hsiu-Chin Lin, who focused on exploring molecular phylogenetic relationships. Meanwhile, Chien-Hsiang Lin studied the application of otoliths and their fossils in fish classification and the reconstruction of paleobiodiversity and biogeography. Taiwan's strength in fish taxonomy research is directly related to its unique geographical location and rich fish diversity. Moreover, the classification of adult fishes and the use of DNA barcoding for species identification of fish eggs and larvae have developed considerably and achieved laudable results. The Taiwan Fish Database has a history of 35 years and is very popular and well-known both in Taiwan and abroad. Taiwan hosted the 7th and 12th Indo-Pacific Fish Conferences in Taipei, in 2005 and 2025, respectively, which attracted many ichthyologists and taxonomists from abroad to engage in intellectual exchanges with domestic scientists. In addition to introducing the aforementioned major scholars engaged in Taiwanese fish taxonomy research and their contributions, this article also briefly summarizes the evolution of the fish classification system, the status of Taiwanese specimen collections, statistics on the number of fish species in the database, types of fish geographical distribution and mechanisms of their formation, the classification of fish eggs and larvae, cooperation and exchanges in fish research between Taiwan and China, and the difficulties and future prospects of fish taxonomy studies. The aim is to chronicle the historical development of fish taxonomy in Taiwan for future reference. However, because the article involves many different aspects, it is impossible to describe them all in detail, and some omissions are likely to occur. It is hoped that any unintentional omissions may be excused and that overlooked facts will be added in future documentation.