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Coral reef decline persists as a global issue with ties to climate change and human footprint. The SeaFlower Biosphere reserve includes some of the most isolated oceanic coral reefs in the Southwestern Caribbean, which provide natural experiments to test global and/or basin-wide factors affecting coral reefs. In this study, we compared coral and other substrate cover (algae, cyanobacteria, and octocorals), along population densities of keystone urchin species from two atolls (Serrana and Roncador Banks), during 1995, 2003, and 2015/2016. We also surveyed benthic foraminifera as a water quality proxy for coral growth in the last period. A steady reduction in coral cover was clearly observed at Roncador's lagoon, but not at Serrana's reefs, with significant differences between 1995 and 2015/2016. Percent cover of fleshy algae decreased significantly also at Roncador between 1995 and 2003 but did not change notably from 1995 to 2016 at Serrana. However, both Banks exhibited a loss in crustose coralline algae from 2003 to 2015/2016. Likewise, a reduction in bottom complexity, measured as bottom rugosity, was evident between 1995 and 2003. Roncador Bank had unprecedented high octocoral densities, which increased almost threefold from 2003 to 2015. In contrast, urchin densities were low in Roncador; only Diadema antillarum increased from 2003 to 2016 in Serrana Bank. The Foraminifera in Reef Assessment and Monitoring (FORAM) Index (FI) in the two Banks was below the range expected for healthy coral reefs. Although both Banks follow a reduction in CCA and CA cover, Roncador Bank also faces an alarming decline in coral cover, urchins and bottom complexity (rugosity) in contrast to increases in octocoral densities and potential loss of resilience and eutrophication suggested by the FI index. These unexpected findings led us to consider and discuss potential outcomes, where these reefs deteriorate (i.e., erode and drown) providing ideal conditions for octocoral growth. Hence, it is of utmost urgency to start monitoring reef budgets, octocorals and nutrient sources.