*Corresponding autor: edlinguerra@gmail.com This checklist contains systematic information of specimens of the cryptobiont assemblages identified by experts of each Phyla and is a complementary material of the research “The use of ARMS to evaluate taxonomic diversity and spatial distribution cryptobiont assemblages of coral reefs in two subregions of the great Caribbean Sea”. The checklist contains 367 morphotypes, 246 species, 86 genera, two subfamily, 26 family, seven class and nine Phyla. For the present research, animals of the appropriate species and quality were selected and the minimum number required to obtain scientifically valid results, as well as anesthetized and deposited in National Collections: Colección Regional de Crustáceos de la Península de Yucatán (SEMARNAT number: YUC-CC-255-11), Colección Regional de Moluscos de la Península de Yucatán (SEMARNAT number: YUC. -INV-240-01-11), Colección Regional de Equinodermos de la Península de Yucatán (SEMARNAT number: DGVS-CC-307-18), Colección Regional de Ascidias de la Península de Yucatán (SEMARNAT number: DGVS-CC-306-18), Colección Regional de Briozoos de la Península de Yucatán (SEMARNAT number: DGVS-CC-308-18), Colección Regional de Cnidarios de la Península de Yucatán (SEMARMAT number: YUC-CC-254-11), Colección Regional de Policládidos de la Península de Yucatán (105 Collection CONABIO) and Colección Nacional del Phyla Porifera “Gerardo Green” of the Universidad Nacional Autónoma de México, Sisal, Mexico (UMDI-Sisal) and within accordance with scientific collection permits: PPF/DGOPA: 295/17, 300/17, 294/17, 293/17, PPF/DGOPA-076/19 issued by Mexico’s State Secretaria de Agricultura, Ganaderia, Desarrollo Rural, Pesca y Alimentación (SAGARPA). CC-BY-NC-N