Chelonid alphaherpesvirus 5 (ChHV5) has been consistently associated with fibropapillomatosis (FP), a neoplastic disease that affects sea turtles globally. The DNA of ChHV5 has been detected in cutaneous and noncutaneous tissues (e.g., lung) of green sea turtles Chelonia mydas with (FP+) and without (FP−) clinical signs of FP, indicating a persistent ChHV5 infection. Previously published and custom primer pairs were used to amplify the fragments of ChHV5 unique long (UL) partial genes (UL30 and UL18) through end‐point PCR from cutaneous tumors (n = 31), nontumored skin (n = 49), and lungs (n = 26) from FP+ (n = 31) and FP− (n = 18) green sea turtles. The DNA of ChHV5 was detected in cutaneous tumors (80.6%, 25/31), nontumored skin (74.2%, 23/31 FP+; 27.8%, 5/18 FP−), and lung samples (91.7%, 11/12 FP+; 100%, 14/14 FP−). The high occurrence of ChHV5 observed in lung samples from FP− individuals was unexpected (14/14), providing the first evidence of ChHV5 DNA presence in lungs of individuals without FP. Our results also revealed high ChHV5 occurrence among the tested cohort (93.9%, 46/49) and suggested that a large proportion (83.4%, 15/18) of FP− green sea turtles had subclinical ChHV5 infections. Hence, our findings support the hypothesis that ChHV5 requires one or more possibly environmental or immune‐related co‐factors to induce FP.