• 107-108，澎湖馬公內灣海域環境品質改善試驗評估計畫，協同主持人。
• 107-108，雲林縣107年度椬梧濕地保育利用暨環境教育推廣計畫，主持人。
• 108，臺南市雙春侵蝕海岸暨地層下陷區背景環境生物及生態保育行動計畫，主持人。
• 108，嘉義縣東石海岸濕地沙洲與潟湖變遷監測計畫，主持人。
• 108，台江國家公園棲地水文資料收集及調控規劃，協同主持人。
• 108-109，108-109年度官田重要濕地(國家級)基礎調查計畫，主持人。
• 108-111，「好美寮濕地養灘工程」(含徵詢計畫及成效監測計畫)設計及監造工作委託技術服務--現況調查及溼地影響說明作業，主持人。
• 109，嘉義縣東石海岸濕地沙洲與潟湖變遷監測計畫(2/3)，主持人。
• 109，北門濕地急水溪中上游地區(學甲濕地)生態背景監測調查計畫，主持人。
• 109，台江國家公園生態多樣性棲地水土環境營造調控試驗示範計畫，協同主持人。
• 109-110，觀塘工業區(港)接收站生態保育執行委員會─觀塘海域漂砂與水質環境保護策略探討，研究人員。
• 109-110，109-110年度北門及八掌溪口重要濕地(國家級)推動環境教育及CEPA行動計畫，主持人。
• 110，台江國家公園四草濕地水域生態與水文調查暨水位營造試驗計畫(2/2)，協同主持人。
• 110，臺南市雙春侵蝕海岸暨地層下陷區背景環境生物及生態保育行動計畫(2)，主持人。
• 110，嘉義縣東石海岸濕地沙洲與潟湖變遷監測計畫(3/3)，主持人。
• 110，110年度第五河川局中央管防洪調適公私協力工作坊，協同主持人。
• 110，110年度臺南市濕地保育與生態遊憩軸帶盤點及整合可行性評估計畫，主持人。
• 110-111，110~111年度北門及八掌溪口重要濕地(國家級)生態與潟湖地形變遷調查及在地溝通工作計畫，主持人。
• 110-111，北汕尾水鳥保護區周緣圳路水文資料收集及水域生態調查計畫，研究人員。
• 111，雙春侵蝕海岸暨地層下陷區背景環境生物及生態保育行動計畫(3)，主持人。
• 111，111年度茄萣濕地生態監測與環境教育推廣計畫，主持人。
• 112，112年度臺南市雙春侵蝕海岸暨地層下陷區環境教育推廣計畫，主持人。
• 112，112年度茄萣濕地生態保育與監測暨棲地維護管理計畫，主持人。
• 112，112年學甲濕地生態調查，主持人。
• 112，彰化海域潮間帶螻蛄蝦族群分布、生殖生物學調查及利害關係人分析計畫，主持人。
• 112-113，鰲鼓重要濕地(國家級)保育利用計畫第一次檢討，主持人。
• 112-113，官田重要濕地(國家級)保育利用計畫第一次檢討，主持人。

期刊論文

• Lin, Feng-Jiau, Hisao-Yuan Chang, Chun-Wen Tsao, Hung-Du Lin and Yih-Tsong Ueng (2021) Population Structures and Diets of Two Species of Pisodonophis (Ophichthidae) from the Southwest Coast of Taiwan. Natural Resources, 12(6), 197-204. doi: 10.4236/nr.2021.126014.
• Ueng, Yih-Tsong, Feng-Jiau Lin, Chun-Wen Tsao, Han-Chang Chen, Wu-Chanl Chang (2021) Sand Grain Size and Organic Matter Concentration in the Intertidal Zones on the Southwest Coast of Taiwan. Natural Resources, 12(4), 108-123. doi: 10.4236/nr.2021.124009
• Kuo, Ai-Ling, Feng-Jiau Lin, Jung-Ting Hsu, Yi-Shin Chan and Yih-Tsong Ueng (2018) The population structure and parasitic relationships of oyster (Crassostrea angulata), Arcotheres sinensis (Pinnotheridae), and Rhopalione sinensis (Bopyridae) at the oyster reefs of western Taiwan. Crustaceana, 91(12): 1433-1451.
• Lin, Feng-Jiau, Wei-Kuang Wang, M.-J. Chen, Hung-Du Lin, Yih-Tsong Ueng (2018) Length–weight relationships of five mullet fish species from the Southern Taiwan coast. Journal of Applied Ichthyology, 34: 162-163.
• Chiang, Tzen-Yuh, Yi-Yen Chen, Teh-Wang Lee, Kui-Ching Hsu, Feng-Jiau Lin, Wei-Kuang Wang, and Hung-Du Lin (2017) Comparative phylogeography of two codistributed endemic cyprinids in southeastern Taiwan. Biochemical Systematics and Ecology, 70: 283-290.
• Ju, Yu-Min, Jui-Hsien Wu, Po-Hsun Kuo, Kui-Ching Hsu, Wei-Kuang Wang and, Feng-Jiau Lin, Hung-Du Lin (2016) Mitochondrial genetic diversity of Rhinogobius giurinus (Teleostei: Gobiidae) in East Asia. Biochemical Systematics and Ecology, 69: 60-66.
• Lin Hung-Du, Po-Hsun Kuo, Wei-Kuang Wang,Yuh-Wen Chiud, Yu-Min Ju, Feng-Jiau Lin, and Kui-Ching Hsu (2016) Speciation and differentiation of the genus Opsariichthys (Teleostei: Cyprinidae) in East Asia. Biochemical Systematics and Ecology 68: 92-100.
• Lin, Hung-Du^#, Feng-Jiau Lin^#, Tzen-Yuh Chiang, and Teh-Wang Lee (2015) The complete mitochondrial genome sequence of Metzia formosae (Cypriniformes, Cyprinidae). Mitochondrial DNA, 26(2): 257-258. [^# authors contributed equally]
• Chuan-Wen Ho, Tzong-Der Tzeng, Tzen-Yuh Chiang, Chih-Yao Li, Feng-Jiau Lin*(2014) Development and characterization of nine polymorphic microsatellite markers from the sword prawn Parapenaeopsis hardwickii using PCR-based isolation of microsatellite arrays (PIMA). Conservation Genetics Resources, 6(3): 547-549. [ *Corresponding author]
• Chiang, Tzen-Yuh, Tzong-Der Tzeng, Hung-Du Lin, Ching-Ju Cho and Feng-Jiau Lin* (2012) Isolation and characterization of polymorphic microsatellite loci from Metapenaeopsis barbata using PCR-based Isolation of microsatellite arrays (PIMA). International Journal of Molecular Sciences, 13: 2763-2768. [ *Corresponding author]
• Lin, Feng-Jiau, Yuan Liu, Zhongli Sha, Ka Hou Chu, Zhaoxia Cui and Tin-Yam Chan (2012) Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes. BMC Genomics, 13: 631.
• Chu, Ta-Jen, Daryi Wang, Hsien-Lu Huang, Feng-Jiau Lin, and Tzong-Der Tzeng (2012) Population Structure and Historical Demography of the Whiskered Velvet Shrimp (Metapenaeopsis barbata) off China and Taiwan Inferred from the Mitochondrial Control Region. Zoological Studies, 51(1): 99-107.
• Chu, Ta-Jen, Hsien-Lu Haung, Chun-Han Shih, Feng-Jiau Lin, and Tzong-Der Tzeng (2011) Population structure and expansion of kuruma shrimp (Penaeus japonicus) in the adjacent waters of Taiwan inferred from intron sequences. African Journal of Biotechnology, 10(74): 16994-17009. (SCI; IF 0.44; Ranking: 137/160)
• Komai, Tomoyuki, Feng-Jiau Lin* and Tin-Yam Chan (2010) Five new species of Axiidae (Crustacea: Decapoda: Axiidea) from deep-water off Taiwan, with description of a new genus. Zootaxa, 2352: 1-28. [ *Corresponding author]
• Komai, Tomoyuki, Feng-Jiau Lin, and Tin-Yam Chan (2009) A new mud shrimp species of Calastacus (Crustacea: Decapoda: Thalassinidea) from the South China Sea. Zootaxa, 2088: 24-30.
• Li, HY. Feng-Jiau Lin, Benny KK Chan and Tin-Yam Chan (2008) Burrow morphology and dynamics of the mudshrimp Austinogebia edulis (Crustacea: Decapoda: Thalassinidea) in Hong Kong and Taiwan soft shores. Journal of Zoology, 127(4): 301-311.
• Tsang, Lin Ming, Feng-Jiau Lin, Tin-Yam Chan and Ka Hou Chu (2008) Molecular phylogeny of Thalassinidea (Crustacea, Decapoda) inferred from nuclear 18S rDNA and mitochondrial 16S rDNA and a proposal for revision of current superfamily classification. Journal of Zoological Systematics and Evolutionary Research, 46(3): 216-223.
• Chiang, Tzen-Yuh, Hung-Du Lin, Cheng-Yu Hung, T.-Y. Chan and Feng-Jiau Lin*. 2008. Isolation and characterization of microsatellite loci in the commercially important mudshrimp Austinogebia edulis (Upogebiidae) using PCR-based isolation of microsatellite arrays (PIMA). Conservation Genetics, 9:1653-1655.
• Lin, Hung-Du^#, Teh-Wan Lee^#, Feng-Jiau Lin^#, Chung-Jian Lin and Tzen-Yuh Chiang (2008) Isolation and characterization of microsatellite loci in the endangered freshwater fish Pararasbora moltrechti (Cyprinidae) using PCR-based isolation of microsatellite arrays (PIMA). Conservation Genetics, 9: 945-947. [ ^# authors contributed equally]
• Chiang, Tzen-Yuh^#, T.-W. Lee^#, Feng-Jiau Lin^#, K.-H. Huang and H.-D. Lin. 2008. Isolation and characterization of microsatellite loci in the endangered freshwater fish Varicorhinus alticorpus (Cyprinidae). Conservation Genetics, 9:1399-1401. [ # authors contributed equally]
• Lin, Feng-Jiau, Tomoyuki Komai and Tin-Yam Chan (2007) A new species of callianassid shrimp (Crustacea: Decapoda: Thalassinidea) from deep-water hydrothermal vents off Taiwan. Proceedings of the Biological Society of Washington, 120(2): 143-158.
• Lin, Feng-Jiau, Tomoyuki Komai and Tin-Yam Chan (2007) First record of the thalassinidean genus Callianopsis de Saint Laurent, 1973 (Decapoda, Ctenochelidae) in the West Pacific, with description of a new species from Taiwan. Crustaceana, 80(10): 1193-1203.
• Lin, Feng-Jiau and Tomoyuki Komai (2006) A new calocaridid shrimp of the genus Calaxiopsis (Crustacea, Decapoda, Thalassinidea) from deep waters off Taiwan. Zoosystema, 28(2): 399-408.
• Lin, Feng-Jiau (2006) Two new axioid shrimps (Decapoda: Thalassinidae) from New Caledonia. Journal of Crustacean biology, 26(2): 234-241.
• Ngoc-Ho, Nguyen, Feng-Jiau Lin and Tin-Yam Chan (2005) New records for the axiid shrimp Eutrichocheles modestus (Herbst, 1796) with discussion on the genera Eutrichocheles Wood-Mason, 1876 and Paraxiopsis de Man, 1905 (Crustacea: Decapoda: Thalassinidea). Proceedings of the Biological Society of Washington, 118(1): 199-208.
• Lin, Feng-Jiau, Nguyen Ngoc-Ho and Tin-Yam Chan (2001) Anew species of mud-shrimp of the genus Upogebia Leach, 1814 from Taiwan (Decapoda: Thalassinidea: Upogebiidae). Zoological studies, 40(3): 199-203.
• Kensley, Brian, Feng-Jiau Lin and Hsiang-Ping Yu (2000) Further records of thalassinidean shrimps from Taiwan (Decapoda: Axiidae and Calocrididae), with descriptions of three new species. Journal of Crustacean Biology, 20 (Special No. 2): 207-217.
• Lin, Feng-Jiau, Brian Kensley and Tin-Yam Chan (2000) The rare axiid geneus Oxyrhynchaxius Parisi, 1917 (Decapoda: Thalassinidea), with a description of a new species from Australia. Journal of Crustacean Biology, 20 (Special No. 2): 199-206.
• 翁義聰、林鳳嬌、童淑珠、鄧伯齡 (2020) 臺灣西南沿海地層下陷區生態熱區與保育策略之探討，濕地學刊，第9巻第1期，73-90。
• 石惠韻、童淑珠、林鳳嬌、翁義聰(2019) 嘉義縣布袋廢曬鹽田之穴居甲殼類調查，濕地學刊，第8巻第1期，55-63。
• 溫志中、林鳳嬌、羅建明、柯正龍、葉秀貞 (2019) 離岸風機金屬腐蝕調查研究，港灣季刊，第113期，88-109。

研討會論文

• 林敬樺、林鳳嬌、黃冠鳳(2023)雙春海岸侵蝕與保安林面積消長之探討，第14屆濕地研討會，臺南，6/-69，2023年9月1日。
• 朱木壽、林鳳嬌、盧韋勳、葉柏志(2023) 北汕尾水鳥保護區周緣圳路水文資料收集調查研究，第14屆濕地研討會，臺南，29，2023年9月1日。
• 張淑蕙、郭品含、張筱筠、黃冠鳳、林鳳嬌、王筱雯、林政偉、鄧伯齡、翁義聰 (2023) 海岸侵蝕與沉降對紅樹林生態系及漁業資源的影響—以臺灣西南海岸為例，第14屆濕地研討會，臺南，34-36，2023年9月1日。
• 羅建明、溫志中、葉秀貞、莊凱迪、黃宇謙、林鳳嬌 (2020) 「離岸風電基地母港海域水質環境及金屬附著生物調查」，第42屆海洋工程研討會，基隆，702-707，2020 年 11 月。
• 林鳳嬌、林敬樺(2020) 「無人飛行載具與三維實景重建應用於濕地地貌調查初探」，第11屆濕地研討會，臺北，36，2020年9月12日。
• 羅建明、柯正龍、溫志中、林鳳嬌、葉秀貞 (2019)，「離岸風場海域腐蝕試驗研究」，第41屆海洋工程研討，會，台南。
• 羅建明、溫志中、林鳳嬌、王俊欽、柯正龍、葉秀貞、邱永芳，(2018)，「離岸風機水下金屬腐蝕機制研究」，第 40 屆海洋工程研討會論文集，高雄，489-494。
• Lin, Feng-Jiau, Hsiu Wen Tso, Jung Ting Hsu, Yih-Tsong Ueng and HsiaoYun Chang (2017) A Comprehensive Investigation for Coastal Situation around Kaohsiung Coastal Area. The 16th International Conference on Civil and Environmental Engineering.
• Li, Chih-Yao, Tzong-Der Tseng, Feng-Jiau Lin^* and Tzen-Yuh Chiang (2010) Population Structure and Genetic of the sword prawn Parapenaeopsis hardwickii in the East China Sea and Taiwan. The Seventh International Crustacean Congress, June 2010, Qingdao, China.
• Cho, Ching-Ju, Tzong-Der Tseng, Feng-Jiau Lin^* and Tzen-Yuh Chiang (2010) Population Structure and genetic variation of the red-spotted prawn Metapenaeopsis Barbata in the East China Sea, South China Sea and Taiwa The Seventh International Crustacean Congress, June 2010, Qingdao, China.
• Li, Chih-Yao, Tzong-Der Tseng, Feng-Jiau Lin and Tzen-Yuh Chiang (2010) Isolation and characterization of microsatellite loci in Parapenaeopsis hardwickii using PCR-based isolation of microsatellite arrays (PIMA). The 2010 Annual Meeting of the Animal Behavior and Ecology, Changhua, Taiwan, R.O.C.
• Lin, Feng-Jiau, Hung-Du Lin, Tin-Yam Chan, Ping-Hang Chung and Tzen-Yuh Chiang (2009) Population structure in the commercially important mudshrimp Austinogebia edulis in Taiwan and Hong Kong revealed by mitochondrial and microsatellite DNA markers. The Crustacean Society Summer Meeting in Tokyo, Japan & the 47^th Annual Meeting of the Carcinological Society of Japan, Shinagawa, Tokyo, Japan.
• Chung, Ping-Hang, Ping-Ho Ho, Tzen-Yuh Chiang and Feng-Jiau Lin^* (2008) Isolation and characterization of microsatellite loci in the endemic fiddler crab Uca formosensis Rathbun, 1921 (Ocypodidae) using PCR-based isolation of microsatellite arrays (PIMA). The 2008 Annual Meeting of the Fisheries Society of Taiwan, Taipei, Taiwan, R.O.C.

專書或技術報告

• 羅建明、王俊欽、溫志中、周偉龍、林鳳嬌、葉秀貞 (2018) 離岸風電水下技術研發。交通部運輸研究所。
• 林鳳嬌 (2018) 生態產業願景化為濕地保育動力—成龍濕地的執行心得。濕地保育電子公報，106第一期：pp 21-23。內政部營建署城鄉分署。
• 林鳳嬌 (2010) 海洋環境之生物多樣性(譯)。法國巴黎演化博物館—演化的偉大長廊 (La Grande Galerie de l’Evolution)。行政院國家科學委員會生物處、農委會特有生物研究保育中心、國立成功大學。
• 林鳳嬌 (2008) 台灣海洋生物多樣性(摺頁)--海蛄蝦。行政院國家科學委員會生物處出版。
• 林鳳嬌、陳天任和游祥平( 1999) 鹿港蝦猴。水族寵物雜誌3: 162-16。