Infectious diseases with complex life cycles or environmental reservoirs are extremely difficult to eradicate. Understanding their evolution (how new variants emerge) and ecology (where they originate and replicate) is therefore key to controlling them. My goal is to change to way we approach infectious diseases, from a perspective of intervention to one of prevention. This is now possible using modern molecular microbial ecology approaches to monitor populations of human pathogens, both in their host and in the environment. My focus is on Cholera, an ancient and often-fatal diarrheal disease with a complex ecology, which still affects 1.4 to 4.3 million people a year, causing between 28,000 to 142,000 deaths. Its causative agent is Vibrio cholerae, a bacterium with aquatic environmental reservoirs. New variants emerge constantly and have so far spread worldwide in three separate waves. We now know that cholera is constantly evolving in its endemic home, the Bay of Bengal, which is the ultimate source of all waves of the current pandemic. I believe that understanding the ecological and evolutionary dynamics of cholera in its natural home will not only save lives locally, but also prevent of its spread abroad.