In Cuba, juvenile green turtles affected by fibropapillomatosis have increased; however, neither animals' life quality nor their habitat quality has been evaluated. Therefore our objectives were to assess green turtles' habitat quality in the Wildlife Refuge "Lanzanillo- Pajonal-Fragoso" and to evaluate the severity of the fibropapillomatosis and the body condition of affected sea turtles. From October/2013 to December/2019, 48 juvenile green turtles stranded or entangled were spotted (19 were measured). Spearman correlation was uses to determine annual variation of juveniles' size. Body condition was assessed based on plastron characteristics and muscle mass. In ten individuals, tumors were counted according to their size and position. Foraging habitat quality was assessed with the Ecological Evaluation Index and the Ecological Status Index using the proportion of opportunistic and late successional macroalgal groups. The presence/absence of seven heavy metals (cobalt, chromium, iron, germanium, mercury, manganese and nickel) was determined in Thalassia testudinum and Syringodium filiforme using X-ray fluorescence spectrometry. Habitat quality was moderate to high according to the ecological index and the presence of Mn, Hg, Fe and Cr in more than 30% of seagrass samples. Fibropapillomatosis prevalence was of 69% (28/41) in stranded individuals and 43% (3/7) in entangled. The severity score was very high in the 52% of animals (13/25). Tumors predominated in the anterior region of their body. Habitat quality may be related with the presence of fibropapilloma since most of afflicted sea turtles where found in stations with moderate quality and the presence of heavy metals.