The glass blennies of Emblemariopsis are found only in the tropical western Atlantic Ocean and the genus is composed of 13 species in the Greater Caribbean region and one species from Brazil. The identity and ranges of the various species are poorly documented and the available keys and species lists are unreliable, mainly due to species descriptions based on few specimens and the very different appearances of immature phases, females, males, and territorial males. The combination of extensive underwater photography and mtDNA sequencing (uniting the phases and delineating species boundaries) clarifies the taxonomy and biogeography of the glass blennies. There are several complexes composed of regional mtDNA lineages, typically with corresponding morphological differences. The red-bannered species complex with orbital cirri has males with red-banded anterior spinous-dorsal fins, and is composed of 7 mostly allopatric species that divide up the Caribbean Sea and Brazil. A complex without orbital cirri or red bands contains 4 allopatric species dividing up the Greater Caribbean. Two other complexes are single species composed of genetically divergent allopatric populations (“genovariants”) with wide ranges in the central Caribbean Sea; the fourteenth species is a Venezuelan endemic. Two new species are described: Emblemariopsis lancea Victor, from the Windward Lesser Antilles, previously misidentified paratypes of E. occidentalis; and Emblemariopsis falcon Victor & Rodríguez, an endemic species to northwestern Venezuela. Two species are synonymized with previously described species: E. arawak with E. leptocirris and E. ramirezi with E. tayrona. A phenetic tree of COI mtDNA barcode sequences of the genus shows deep divergences between most species, except for two pairs of species which share lineages, as well as genovariants also showing deep divergences. Florida, the Gulf of Mexico, and the ABC Netherlands Antilles, have only a single glass blenny species, while other locations, such as Belize and the U.S. Virgin Islands, have as many as 4 species.