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Composition of fish assemblages is recognized as an indicator of ecosystem health, habitat degradation, and ecosystem productivity. Fish community structure has been associated with coral coverage and diversity. Recent events, such as climate change, have caused extensive coral bleaching, resulting in a loss of habitat for fish and ultimately reduced fish abundance. This study was conducted to assess fish assemblages on the Mesoamerican Barrier Reef in Roatán, Honduras. The standard Roving Diver Technique was used to locate fish assemblages at two depths, 9.14 m and 15.24 m, across five dive sites. Fish communities were characterized for species presence and abundance and each dive site was sampled twice. The Kruskal-Wallis was used to determine the statistical significance between the two depths. The Shannon-Weiner index of diversity was used to measure the diversity between the two depths and the dive sites. Non-metric multidimensional scaling was used to look at how species composition varies by depth and dive site. We found no significant differences in species richness between the two depths surveyed (p = 0.93); however, there was a significant difference between the study sites. Bear’s Den had the lowest species diversity out of all the sites, and Fish Den had the highest species diversity. Fish Den and Pillar Coral each have a unique species composition which differ in comparison, to the other sites. This study provides a baseline description of reef fish community structure. Future studies can use these results to measure changes in community structure over time.