Earth biodiversity is impacted by a wide range of environmental changes originating from dynamics at local(e.g. deforestation, urbanization) and regional (global climate changes) scales that have led to loss ofbiodiversity during the last decades. Biodiversity sustains ecosystem services (e.g. food security,epidemiological control) and its contribution in maintaining productive and resilient ecosystems is now widelysupported by empirical observations. Biodiversity, however, is not evenly distributed on Earth and someareas of exceptional richness facing severe anthropogenic perturbations have been identified as biodiversityhotspots. In Southeast Asia (SEA), several of the largest and most endangered hotspots have beenrecognized. The confusion that reigns over freshwater biodiversity in SEA, however, bridles conservationeffort and ecological climate change research.FRESHBIO aims at integrating human and life sciences with the objectives: (1) to break ground inbiodiversity monitoring by establishing new standards in biodiversity sciences, (2) to pioneer ecological andclimate change research in insular SEA through historical and monitoring approaches, (3) to explore manand biosphere relationship by assessing the impact of environmental changes on the biodiversity andcommunities at several spatial and temporal scales. With these objectives, FRESHBIO aims at: (1) framingbiodiversity research and monitoring through the development of automated DNA-based methods of speciesidentification and environmental DNA approaches, (2) assessing the ecological (community assembly anddynamics) and evolutionary (expansion vs. contraction) states of aquatic biodiversity in SEA insular hotspotsresulting from heterogeneous geological and biotic contexts, (3) assessing the impact of environmentalchanges on biodiversity through a mapping approach as well as identifying adaptive strategies andevaluating the resilience of local communities in front of biodiversity loss through a diachronic approach.FRESHBIO is proposed by a consortium of researchers from France, Germany, Philippines and Indonesiawith a long-standing interest on the ecology and evolution of insular SEA freshwater biotas as well as itsconservation and sustainable use. This project offers a unique opportunity to regionalize biodiversityresearch in insular SEA and helps break through the taxonomic impediment for large-scale assessments ofthe state of freshwater biodiversity. Compliant with the Access and Benefit Sharing principle of theConvention on Biological Diversity, FRESHBIO matches several of the national priorities of the participantssuch as the development of solutions for stopping biodiversity loss and concepts for sustainable usestrategies to ensure essential ecosystem services, the development of scientific networks to increase theacademic competitiveness of developing SEA partners and scientific innovation in a changing world.