This manuscript reviews disease syndromes that have become significant aquatic animal health issues within the United States since 2003. The emergence of Viral Hemorrhagic Septicemia (VHS) disease among wild fish in the Great Lakes is probably the most problematic and political issue. The emergence of this pathogen resulted in the issuance of a 2006 VHSV Federal order that placed restrictions on the movement of certain species of fish in the eight states that border the Great Lakes (New York, Pennsylvania, Ohio, Indiana, Illinois, Michigan, and Wisconsin and Minnesota) as well as the movement of live fish into the United States from the Ontario and Quebec Provinces, Canada. Spring Viremia of Carp (SVC) was identified for the first times in the United States during 2002. It was diagnosed as the source of mortality among koi at a private facility in North Carolina as well as from feral carp in Cedar Lake (WI). In 2004, Koi Herpesvirus (KHV) killed 8,000 adult common carp (Cyprinus carpio) in the Chadakoin River (NY); it reoccurred the next year within Chautauqua Lake (NY), killing an estimated 25,000 carp (20–30 lbs. apiece). During the summers of 2007 and 2008, KHV epizootics also occurred among carp in Ontario (Canada). Finally, outbreaks of epizootic shell disease in American lobster (Homarus americanus) have generated concern along the southern New England coast and eastern Long Island Sound. The prevalence and severity of shell disease have increased within inshore areas of southern New England and resulted in significant decreases in lobster catches and marketability.