Epidemics among New Zealand sea lion pups in the 2001/02 and 2002/03 breeding seasons highlight the importance of examining the role of disease in the population dynamics of this threatened species. The pathogen implicated in both events was the gram negative bacterium Klebsiella pneumoniae. Isolates from both seasons were genetically indistinguishable, suggesting that the events were caused by a single introduction of an epidemic strain of the pathogen. The events were characterized by a sharp rise in pup mortality approximately three weeks after the start of the pupping season. On post mortem examination, affected pups had one or more of the following lesions: acute suppurative arthritis or polyarthritis, cellulitis, peritonitis, pleuritis, or meningitis. Adults were not apparently affected. Prior to the appearance of Klebsiella, mortality to mid January (~ six weeks of age) among pups was 6.2%, with mortality by mid