Caribbean coral reefs in the1950s through to the early 1970s were viewed as robust and stable ecosystems, and not considered threatened in any way by a human-dominated world. However, in 1982-1983, in the western Atlantic region including the Caribbean basin, the sea-urchin Diadema antillarium, a keystone grazer, died off suddenly. This event, coupled with over-fishing of herbivores and multiple coral-bleaching episodes in the Caribbean region dating back to the 1970s triggered a phase shift from a coral-dominated to an algal-dominated environment. The decline of coral reefs, including fisheries, in the Caribbean region, had fuelled much debate, as several scientists had hypothesized that, by the time humans started studying the coral reefs in the 1950s, the reefs were already overfished and in a degraded state. However, concerns were raised mainly on noticing the gradual loss of the goods and services provided by the coral reefs. With >275 million people in the global tropics living at <30-km distance away from coral reefs, of which >43 million of those people residing in the Caribbean basin has raised the alarm about the loss of coral cover from ~50% average 4 decades ago to a mere regional average of ~12% presently. Though this decline can be attributed to several factors, including the consequences of climate change, over-fishing, ocean acidification, and destructive cyclones, it has spurred and driven coral reef researchers to understand the ecology and biology of these ancient animals better. urthermore, in the last few decades, coral reefs’ ability to function while facing these threats has prompted additional research to understand the ecological and biological attributes of coral reefs and their associated organisms, such as reef fish populations, to ascertain what drives their relationship. However, those underpinning biological and ecological metrics have seemingly eluded coral reef scientist over the past four decades. In September 2009, the Cayman Islands coral reefs experienced a localized acute coral bleaching event with water temperature > 30 C for six weeks. This event was caused by a whirlpool of hot water originating off of the island of Cuba southern shelf. Bleaching was observed down to a depth of 100 m using a remotely operated underwater vehicle (ROV). Furthermore, satellite water temperature data from the National Oceanic and Atmospheric Administration (NOAA) showed that water temperatures extended to a depth of 450 m. The coral reefs of the Cayman Islands recovered without any measurable coral mortality; however, there was a notable decline in algal mortality for the island of Grand Cayman. Furthermore, in both 2015 and 2016, the global marine heatwave, the longest ever on record that effected greater than one-quarter of the ocean surface, with devastating consequences for marine ecosystems globally had a negligible effect on the coral reefs of the Cayman Islands. Data was collected on the Benthos and their fish assemblages over years (2009–2012), islands, coast (North, South and West) habitats (deep and shallow) and protection status (MPA and non-MPA) at 55 sites across the 3 Cayman Islands; Grand Cayman (GCM, n=27), Little Cayman (LC, n=16) and Cayman Brac (CB, n=12). Total fish biomass differed significantly over the years, showing an overall strong reserve effect (p = 0.001). A significant spill-over effect for the shallow terrace reef on the northern boundary of the MPA in GCM was detected in the years 2009 (P<0.01) and 2011(P<0.01) No spill-over was evident on the deep terrace reef of any the islands, possibly due to residents able to fish anywhere beyond the 24 m depth contour. With more than 50% of the total variance explained, the analysis of principal coordinates (PCO) showed that the functional differences between MPA and non-MPA regarding fish assemblages across the habitats and islands were highly correlated (p = 0.8) indicative of a positive linear relationship with 4 species of fish: (1) Holacanthus tricolour, (2) Sparissoma aurofrenatum, (3) Anisotremus Surinamensis and (4) Kyphosidae spp. The community structure of fish significantly differed across years on all islands (p < 0.001). The fish ommunities were found to be most similar between the years 2009 and 2010. However, their differences in community structure increased over time, indicating that MPA’s effects were not consistent across years on all islands. The temporal and spatial changes in the benthic community structure documented during the period of study were complex, and their trajectories depended on a combination of factors such as the habitat type, coast, and island, including protection. SIMPER analysis revealed the largest average dissimilarities to be GCM for the years 2011 and 2012 (54.4%, driven by macroalgae, dead coral and pavement), whereas the lowest was found between the years 2009 (30.9 %, turf, and macroalgae) and 7 2012 (40.5 %, turf algae) in Little Cayman. Differences between turf and macroalgae consistently explained 61% to 79% of the average similarities recorded across the Cayman Islands during the study period. The results clearly show that 2011 was a particular year that introduced significant variation to the benthos community structure, particularly for the island of GCM and CB. Higher values of live coral cover (15–20%) was noted in the deeper and shallower habitats of LC and CB, with no evident trends recorded between the areas with different levels of protection. Lower coral cover was found in the shallow habitats around the GCM, regardless of protection status. There was a clear spatial pattern for macroalgae, showing higher cover in the deeper habitats of LC and CB (50–70%), as compared to the shallow habitats of GCM (34–46%). Higher cover of turf algae was normally associated with the shallower habitats of all three islands, but more so LC and CB. Results from Bio Env analysis clearly showed that both benthic and the fish community assemblages were significant, but weakly correlated (BEST, Rho = 0.26, p = 0.01). Variation of the three combined benthic variables: zoanthids, tunicates, and dead gorgonians better fit with the documented changes in the fish community structure across coasts, islands, habitats, years, and protection status. Additionally, the linear model supported that only the zoanthids, dead gorgonians and the cover of other benthic organisms were significantly correlated with changes in the fish community structure, possibly because they were being used as a food resource. However, the DbRDA plot illustrated that changes in the benthic community structure did not fully explain the observed variation in the fish community structure, suggesting some other metric not studies in this thesis is responsible. Results indicate that the MPA’s of the Cayman Islands are playing a central role in increasing the biomass of key herbivores and carnivores over time. Data collected indicate that the benthic community structure was extremely variable between habitats; this factor explaining more variation compared to the level of protection and suggest that the benthic community structure was a poor predictor for explaining the differences of the fish communities associated to MPAs and non-MPA’s across the Cayman Islands. This study aimed to assess the status and evaluate the effects of protection on the benthos and their fish assemblages of the marine protected areas in the Cayman Islands after 26 years of being actively enforced. It represents an important step in addressing and understanding the Marine Protected Area’s ecological function and performance. It is the intent that the results from this study be used to address the present human usage and increasing pressures on the coral reefs of the Cayman Islands. This includes making recommendations based on results for a new network of MPAs, as the current model has become obsolete, making the MPA’s of the Cayman Islands more “ fit for purpose” in the 21st century for the people of the Cayman Islands.