Understanding the genetic and ecological factors which support the periodic emergence of toxigenic Vibrio cholerae causing outbreaks of cholera in regions where the disease is endemic, is vital to develop preventive measures. Besides environmental factors which are not precisely defined, bacteriophages, and horizontally transmissible genetic elements are known to have a significant role in the epidemiology and evolution of the pathogen. Cholera epidemics are also known to be self-limiting, and hence identifying natural factors which contribute to the collapse of epidemics may have important implications in controlling the disease. Phages have been shown to play a crucial role in modulating cholera epidemics, and enhance V. cholerae evolution through a bactericidal selection process which favors the emergence of new clones.