One of the greatest problems concerning marine biodiversity conservation management is the lack of knowledge of species, abundance and distribution as well as a lack of qualified taxonomists to study the fauna. The echinoderms from the shallow waters of Puerto Rico is similarly abundant and diverse to the other islands of the Caribbean region, but previous studies are few and old. The existing information is reduced to two reports published at the beginning of the 20th century, and some theses and reports published near the end of the century. The principal goal of this study is to update the echinoderms inventory from shallow waters of Puerto Rico based on examination of reference material in the echinoderms collection of the National Museum of Natural History (NMNH), Washington, D. C. and the echinoderms of the Invertebrate Collection of the Marine Department, Puerto Rico University, Mayagüez Campus. In addition, extensive material was collected from La Parguera to the southeastern region of Puerto Rico from coral reefs and sea grass beds with a variety of sandy or rocky substrates. Within this study, a total of 103 species are reported from the shallow waters of Puerto Rico of which 6 species belong to the Class Crinoidea, 14 to the Class Asteroidea, 41 to the Class Ophiuroidea, 14 to the Class Echinoidea and 28 to the Class Holothuroidea. A total of 10 species are reported for the first time, and 52 specific localities are provided. The zoogeographical affinities of the shallow waters of Puerto Rico are discussed in comparison with other studies from the Caribbean.