Marine turtle fibropapillomatosis is associated with chelonid fibropapilloma-associated herpesvirus (C-FP-HV) and commonly affects juvenile green turtles (Chelonia mydas) in neritic (nearshore) habitats. Green turtles have a complex life history, characterized by shifts in trophic level as well as habitat during ontogeny. Thus, several hypotheses can be proposed for when turtles become infected with C-FP-HV. They may acquire the virus at an early stage in the life cycle, including prenatal, hatchling, or the posthatchling pelagic stages. Alternatively, they may become infected later in life after they emigrate from the open ocean to neritic habitats. Each hypothesis generates predictions about the spatial distribution of genetic variants of C-FP-HV among nearshore sites within a region. Sequencing of polymerase chain reaction–amplified viral DNA from fibropapillomas of individual turtles was used to genotype the viral variants present in marine turtles from different coastal areas in Florida. We found four distinct virus variants (A, B, C, and D), two of which (A and C) were present in multiple turtle species. Green turtles in Florida were infected with variants A, B, and C. Variant A was found in green turtles from all three areas. Outside the Indian River Lagoon, variant A was most commonly detected and was found in >94% of diseased green turtles and 70% of loggerhead sea turtles (Caretta caretta) in the Florida Bay/Florida Keys. However, in the Indian River Lagoon, variant B was found in >94% of affected green turtles. Variant B was not detected outside of the Indian River system. Chi-square analysis strongly supported (P<0.001) an association between viral variant distribution in green turtles and location. On the basis of the assumption that juvenile green turtles found in Florida's west-central coast, Florida Keys, and Indian River Lagoon areas represented recruits from a mixed pelagic population, we expected that the distribution of viral variants in these turtles would be relatively homogeneous among locations; this would correspond to infection in the earlier phases of their life cycle. The heterogeneous distribution of viral variants in green turtle tumors from different Florida coastal locations strongly supports the hypothesis that, during epizootics, turtles are infected with specific C-FP-HV variants after they arrive as juveniles in neritic habitats. The conclusion that C-FP-HV is acquired after turtles recruit to nearshore habitats should help focus further research efforts on understanding the mechanisms of transmission and raises the possibility that the effect of fibropapillomatosis on turtle populations might be reduced by management strategies designed to break the cycle of transmission in these locations.