The research project BIOHOPSYS aims at investigating the local impacts of environmental changes (e.g. habitat modification, climate change) on zoonotic and vector-borne diseases (nearly 60% of emerging infections), in relation to biodiversity heterogeneity and change. The programme is localized in French Guiana (FG), both a hotspot of biodiversity, particularly at threat due to land use, climate and demographic changes, and a region with high potential risk of zoonotic and vector-borne emerging diseases in the near future. FG is a specifically well suited model to investigate local impacts of environmental changes on the interactions between biodiversity and infectious diseases due to its geographical localization near the equator line and its socio-economical conditions which mirror in part those of a developing country. The objectives of BIOHOPSYS are (1) to analyze five infectious diseases and their hosts in relation to biodiversity modification and environmental change, (2) to model their transmission dynamics according to habitat and ecosystem alteration, climate change and biodiversity loss, and (3) to propose scenarios of disease transmission accordingly. Analyses of local situations and their evolution will help to inform policy-makers and public health authorities on conditions at higher risks for increasing disease transmission and spread in humans.