Fibropapillomatosis (FP) is an infectious, neoplastic disease of sea turtles in circumtropical coastal ocean waters worldwide. FP tumors can cause debilitation by hampering turtles feeding, movement, and vision, and visceral tumors can cause organ failure. Fibropapillomatosis is panzootic in free-ranging green sea turtles (Chelonia mydas), and is also a concern in rehabilitating turtles because it requires extensive quarantine measures and complicates prognoses. An alphaherpesvirus, designated chelonid fibropapilloma-associated herpesvirus (CFPHV), is consistently identified in FP tumors, and cell-free tumor extracts successfully transmitted the disease. CFPHV was also identified in some normal turtles via serology and polymerase chain reaction (PCR). Despite numerous studies, the actual pathogenesis of CFPHV, its nature of persistence or latency, and its transmission dynamics are not yet fully understood. The objective of this study was to investigate aspects of CFPHV natural history dynamics in free-ranging and rehabilitating green turtles with and without FP. First, nested PCR was used to identify CFPHV DNA in skin from tumored and non-tumored, free-ranging green turtles, and combined with laser capture microdissection to identify CFPHV DNA in microscopically separated epidermis and dermis sections of non-tumored skin. A retrospective case series analysis was performed to describe the biology and survival rates of rehabilitating turtles with FP, and evaluate clinical parameters as survivorship predictors. To investigate the relationship between CFPHV loads and clinical disease, and identify potential routes of viral shedding, a quantitative PCR (qPCR) assay was developed, validated, and applied to various biological samples taken from tumored and non-tumored, free-ranging and rehabilitating green turtles. The qPCR data provide relevant, novel evidence for CFPHV DNA localization and mobilization in symptomatic and asymptomatic turtles. CFPHV DNA presence in blood cells may represent a critical viral life cycle phase and transport mechanism, and CFPHV DNA in urine suggests a previously unknown route of transmission. Quantitative CFPHV DNA data also show that, in addition to cutaneous tissues, kidney and nerve cells play a role in CFPHV pathogenesis. Practical application of the presented information will aid in the evaluation of symptomatic and asymptomatic turtles, helping to prevent transmission opportunities among captive turtles and informing management decisions for free-ranging populations.