A first workshop held within the framework of the PathodivSEA project has been the occasion to identify the major research challenges regarding the emergence of zoonotic infectious diseases in South East Asia and the spread of pathogens responsible from those diseases. Based on supporting evidences indicating the zoonotic origins of those diseases, it appeared urgent to investigate the factors controlling the pathogens-human interface by addressing the “One Health” concept which integrates the study of human and animal health with conservation medicine. The necessity of pathogen, vector and reservoir identification (barcoding), pathogens and other tissues' preservation (biobanking) and open databases creation (ebanking) has been recognized, along with the importance of ethical and legal considerations.