This study was conducted in the Jardines de la Reina National Park, Cuba. The health of the communities of corals and crustose coralline algae was studied in the years 2001, 2012 and 2017. The probable effect of hurricanes and sea surface temperature on these communities was also assessed. The area was only affected by three hurricanes and a tropical storm from 2000 to 2017. Sea surface temperature showed an increasing trend (by 0.03°C). The highest percentage of old mortality was recorded in 2001 (74% on the fore reef and 53% on reef crests) and the lowest of recent mortality in 2012 (0.03% on the fore reef and 0.17% on reef crests). Coral cover increased on the fore reef by between 3% and 2% in 2017 in comparison with 2001 and 2012. On the reef crests, the highest cover percentage was in 2001 (14.8%). Unlike local stressors, it was determined that hurricanes and sea surface temperature have likely negatively affected the coral reefs, particularly on reef crests. Both habitats have shown resistance and/or recovery capacity from the impacts suffered after 2001, which suggests some level of resilience.