Inshore bays are key foraging grounds for immature green turtles Chelonia mydas. At these confined areas, capture-mark-recapture (CMR) programs generate valuable information that can be used to estimate vital rates, essential for the effective conservation of this endangered species. We compiled the CMR history profiles of 273 individuals from 13 yr of in-water surveys and employed the Cormack-Jolly-Seber model to estimate the survival probabilities of green turtles in 2 neritic bays at Culebra municipality, Puerto Rico. The CMR profiles were grouped into 2 size classes: juvenile and subadult. No adults were captured during the study. We found no significant differences in survival probability between the green turtles occupying each bay. We also assessed the survival probability of fibropapillomatosis (FP)-afflicted turtles versus FP-free turtles and found no significant differences among these groups. However, there was a significant difference in survival between the 2 size classes. Juveniles showed a higher survival probability (0.8322, 95% CI = 0.7875 to 0.8690) than subadults (0.5290, 95% CI = 0.3851 to 0.6682). The low survival of subadults is potentially biased by the permanent emigration of some of these individuals. Previous studies have shown that larger immatures leave shallow protected bays and occupy deeper open waters, sometimes associated with adults. Juveniles seem to be resident, and their survival rate can serve as a reference value for viability analysis. This is the first study on the survival of green turtles in the West Indies. © 2011 Inter-Research.