Shallow water zooxanthellate coral reefs grade into ecologically distinct mesophotic coral ecosystems (MCEs) deeper in the euphotic zone. MCEs are widely considered to start at an absolute depth limit of 30m deep, possibly failing to recognise that these are distinct ecological communities that may shift shallower or deeper depending on local environmental conditions. This study aimed to explore whether MCEs represent distinct biological communities, the upper boundary of which can be defined and whether the depth at which they occur may vary above or below 30m. Mixed-gas diving and closed-circuit rebreathers were used to quantitatively survey benthic communities across shallow to mesophotic reef gradients around the island of Utila, Honduras. Depths of up to 85m were sampled, covering the vertical range of the zooxanthellate corals around Utila. We investigate vertical reef zonation using a variety of ecological metrics to identify community shifts with depth, and the appropriateness of different metrics to define the upper MCE boundary. Patterns observed in scleractinian community composition varied between ordination analyses and approaches utilising biodiversity indices. Indices and richness approaches revealed vertical community transition was a gradation. Ordination approaches suggest the possibility of recognising two scleractinian assemblages. We could detect a mesophotic and shallow community while illustrating that belief in a static depth limit is biologically unjustified. The switch between these two communities occurred across bathymetric gradients as small as 10m and as large as 50m in depth. The difference between communities appears to be a loss of shallow specialists and increase in depth-generalist taxa. Therefore, it may be possible to define MCEs by a loss of shallow specialist species. To support a biological definition of mesophotic reefs, we advocate this analytical framework should be applied around the Caribbean and extended into other ocean basins where MCEs are present.