The majority of emerging pathogens has an environmental origin. These pathogens are increasing in incidence and geographic distribution. Because of the continuous worldwide population growth, and global changes, the emergence of pathogens will continue to intensify, particularly in tropical areas where demographic growth is uncontrolled and socioeconomic and environmental changes rapid. Using a set of case studies, we look at the role of biodiversity alteration on zoonoses emergence and transmission routes, as well as the existing links between climate variability and pathogen emergence. Pathogen emergence and transmission are closely associated with habitat alterations and vector or host-species changes. Because of environmental changes, pathogens that were previously in a dynamic equilibrium, with local host communities in a pristine habitat, without human contact, are now redistributed locally, and over long distances, owing to increasing global pathways. Thus, we aim to characterize the environmental determinants of pathogen transmission in the tropics.