Over the half-century since the original Alligator Reef survey, there have been great advances in the taxonomy of Greater Caribbean reef fishes, with numerous changes in scientific names and classification. As part of the update these changes are addressed so as to bring the list to current status.
In 2013 the junior authors (REEF Advanced Assessment Team members) undertook a four-year census of the fishes of the area with a goal to photo-document as many of their sightings as possible. This effort has subsequently entailed 1039 combined dives devoted to fish counts, photographic documentation, or both. During these surveys, they have photographed 278 of the species reported by Starck (1968) plus 35 additional and/or newly described or reclassified species not recorded in the earlier study.
An update of the checklist of fishes of Alligator Reef and environs some fifty years later provides an unparalleled opportunity to evaluate the species richness for a limited reef area, as well as a unique opportunity to explore changes in diversity over a half-century time scale. In the updated study the authors added 107 species and subtracted 5 from the original total of 516 species: thus the checklist now totals 618 species, of 122 families, the most recorded for any similarly sized area in the New World. The additional species records are made up from a number of subsequent collections as well as from a comprehensive effort by the junior authors.
Among the other databases of relevance to the study area used for comparison, the Smithsonian Tropical Research Institute (STRI) Shorefishes of the Greater Caribbean by D.R. Robertson & J. Van Tassell and that of the Reef Environmental Education Foundation (REEF).
REEF maintains an online database of worldwide visual fish-count surveys conducted by volunteer researchers and fish-count enthusiasts. While such surveys are biased towards easily observed species, they are indicative for a large portion of the reef fish fauna and comprise a valuable source of comparative information (Schmitt & Sullivan 1996, Pattengill-Semmens & Semmens 2003, Holt et al. 2013). The local REEF data includes that of the Estapés, who have conducted 185 roving-diver REEF surveys on Alligator Reef. An additional 1807 surveys at 94 sites in the study area have also been conducted by other REEF volunteers (as of July, 3, 2016).