| Start Date | Title | P-Investigator | Funding Organization/經費來源 |
| 2022 | 陽明山國家公園瑪鋉溪上游之溪流魚類群聚生態監控及其繁殖期調查計畫II | I-Shiung Chen | Yangmingshan National Park |
| 2022 | 111-112 年度中央管流域生態固定樣站調查—北中東區 | I-Shiung Chen | Water Resources Planning Institute |
| 2021 | 臺灣東北部岸際生物樣本採集調查專業服務案 | I-Shiung Chen | National Academy of Marine Research |
| 2021 | 110年強化與東協及南亞國家合作交流計畫 | I-Shiung Chen | Ministry of Education |
| 2021 | Studies on the integration of fish farming zones and its fishing ground environmental improvement | I-Shiung Chen | Fisheries Agency,COA, Executive Yuan |
| 2021 | 示範海域海洋生物資訊蒐集及資源調查-北部海域_魚類調查及水質分析 | I-Shiung Chen | National Academy of Marine Research |
| 2020 | 澎湖南方四島國家公園魚類生態圖鑑製作 | I-Shiung Chen | Marine National Park Headquarters |
| 2020 | 109-111年度「陽明山國家公園瑪鋉溪上游之溪流魚類群聚生態監控及其繁殖期調查計畫」案 | I-Shiung Chen | Yangmingshan National Park |
| 2020 | 臺灣岸際生物資源調查專業服務案 分支計畫一 魚類調查及珊瑚及棘皮動物調查與海域水文調查 | I-Shiung Chen | National Academy of Marine Research |
| 2020 | 第三作液化天然氣接收站建港 及圍堤造地工程施工期間環境 監測河口生態調查 | I-Shiung Chen | Institute of Marine Biology |
| 2020 | Studies on the integration of fish farming zones and its fishing ground environmental improvement | I-Shiung Chen | Fisheries Agency,COA, Executive Yuan |
| 2019 | 陽明山國家公園溪流魚類生態水族特展規劃與魚類採集飼育計畫 | I-Shiung Chen | Yangmingshan National Park |
| 2019 | Studies on the integration of fish farming zones and its fishing ground environmental improvement-2 | I-Shiung Chen | Council of Agriculture,Executive Yuan |
| 2019 | 瀕危淡水魚種的繁養殖保種規劃與族群生態調查研究 | I-Shiung Chen | Forestry Bureau, COA, Executive Yuan |
| 2018 | The investigation and conservation strategies of fish and crustacean eco-resource in the river basin of Yangmingshan National Park, 106 ~ 107 (2/2) | I-Shiung Chen | |
| 2017 | 陽明山國家公園溪流各流域魚類及甲殼類生態資源調查及保育策略規劃(1/2) | I-Shiung Chen | Yangmingshan National Park |
| 2015 | Monitoring Marine Fish Fauna, Species Diversity, Cummunity Change and Database Establishment in Keelung (III) | I-Shiung Chen | National Science and Technology Council |
| 2014 | Monitoring Marine Fish Fauna, Species Diversity, Cummunity Change and Database Establishment in Keelung( II ) | I-Shiung Chen | National Science and Technology Council |
| 2014 | Conservation and Ecology Survey of Freshwater Eel Habitats with Evaluation of the Resources | I-Shiung Chen | Council of Agriculture,Executive Yuan |
| 2013 | Morphology, taxonomy, interrelationships and molecular phylogeography and phylogenetics of nemacheiline loaches, with special emphasize on the genera Orthrias and Triplophysa | I-Shiung Chen | National Science and Technology Council |
| 2013 | Effects of Global Change on Ocean Biogeochemistry and Ecosystems in the Seas Surrounding Taiwan in the Northwest Pacific (I)- Research of Coral-Reef Fish Communities and DNA Molecular Identification of Larval Fishes | I-Shiung Chen | National Science and Technology Council |
| 2013 | Monitoring Marine Fish Fauna, Species Diversity, Cummunity Change and Database Establishment in Keelung (I) | I-Shiung Chen | National Science and Technology Council |
| 2012 | Morphology, Taxonomy, Interrelationships and Molecular Phylogeography and Phylogenetics of Nemacheiline Loaches, with Special Emphasize on the Genera Orthrias and Triplophysa | I-Shiung Chen | National Science and Technology Council |
| 2012 | Effects of Global Change on Ocean Biogeochemistry and Ecosystems in the Seas Surrounding Taiwan in the Northwest Pacific (I)- Research of Coral-Reef Fish Communities and Dna Molecular Identification of Larval Fishes. | I-Shiung Chen | National Science and Technology Council |
| 2011 | Morphology, Taxonomy, Interrelationships and Molecular Phylogeography and Phylogenetics of Nemacheiline Loaches, with Special Emphasize on the Genera Orthrias and Triplophysa | I-Shiung Chen | National Science and Technology Council |
| 2011 | The Digital Collection Study of Fish Specimens and Natural Habitat Images of Fishes from Taiwan and China in National Taiwan Ocean University (II) | I-Shiung Chen | National Science and Technology Council |
| 2010 | The Digital Collection Study of Fish Specimens and Natural Habitat Images of Fishes from Taiwan and China in National Taiwan Ocean University | I-Shiung Chen | National Science and Technology Council |
| 2009 | 「瑪陵坑溪、友蚋溪、暖暖溪及草濫溪全流域冬春二季生態調查」委託案 | I-Shiung Chen | Keelung City Government |
| 2009 | Studies of Species Biodiversity, Speciation Patterns, and Molecular Phylogenetics of Stream Benthic Fishes in Taiwan and Hainan Island, China | I-Shiung Chen | National Science and Technology Council |
| 2008 | Establishment of Native Indicators from Aquatic Animal Species and Monitoring of River Fish (II) | I-Shiung Chen | National Science and Technology Council |
| 2008 | Studies of Species Biodiversity, Speciation Patterns, and Molecular Phylogenetics of Stream Benthic Fishes in Taiwan and Hainan Island, China | I-Shiung Chen | National Science and Technology Council |
| 2008 | 「瑪陵坑溪、友蚋溪、暖暖溪及草濫溪全流域生態夏秋二季調查暨深澳坑溪及外木山小溪魚類及蝦蟹類先驅調查」委託調查案 | I-Shiung Chen | Keelung City Government |
| 2007 | Study on Diapausing Stage Resistance for the Elaboration of a New Biotechnology to Prevent the Spreading of Invasive Species with Ship's Ballast Waters and Sediments | I-Shiung Chen | National Science and Technology Council |
| 2007 | The Digital Collection Study of Fish Specimens and Natural Habitat Records of Fishes in National Taiwan Ocean University | I-Shiung Chen | National Science and Technology Council |
| 2006 | Study on Diapausing Stage Resistance for the Elaboration of a New Biotechnology to Prevent the Spreading of Invasive Species with Ship's Ballast Waters and Sediments | I-Shiung Chen | National Science and Technology Council |
| 2006 | Study on the Fishes Ecological Impact of Animal Releasing (II) | I-Shiung Chen | National Science and Technology Council |
| 2005 | Systematics, Geographical Distribution and Molecular Phylogenetics of Rhinogobius from Taiwan and Southeastern China (III) | I-Shiung Chen | Institute of Marine Biology |
| 2005 | Study on Diapausing Stage Resistance for the Elaboration of a New Biotechnology to Prevent the Spreading of Invasive Species with Ship's Ballast Waters and Sediments | I-Shiung Chen | National Science and Technology Council |
