The cleaner and the related striped sponge goby species have a high modal median-fin ray count of D-VII,12 A-11, shared with few other related species. The cleaner gobies are presently considered to be Elacatinus, but have been considered Gobiosoma in the past and are often listed as such in the literature. Amongst the cleaners, there are few exceptions to this modal median-fin ray count: E. oceanops can have D-VII,13 and/or A-12, E. phthirophagus has D-VII,11 and E. chancei has A-10. Pectoral-fin ray counts vary but mostly overlap. Some Tigrigobius gemmatus and the occasional specimens of several other Elacatinus/Gobiosoma would share the combination of 12 second-dorsal-fin elements and 11 anal-fin elements.
It is likely that larval cleaner/sponge gobies have a similar or identical appearance and identification would depend on location and DNA sequencing. Unlike most other Caribbean reef fishes, the cleaner/sponge gobies have restricted ranges to varying degrees and thus location is critical for species identifications. In addition, habitat is an important distinction, with one set of species skating around on live coral heads and usually abundant in shallow water and another set living in and around sponges and often in deeper water. The coral-associated cleaners are typically more common and conspicuous on reefs and include E. evelynae, E. genie, E. illecebrosus (not E. illecebrosum), E. oceanops, E. prochilos, E. lobeli, and E. randalli. The deeper sponge cleaner gobies are typically less conspicuous and include E. chancei, E. horsti, E. xanthiprora, E. colini, E. lori, E. louisae, and E. tenox. Two very curious micro-endemic species hover in groups over corals, quite unlike the rest of the group: E. atronasus from the Exuma Sound area of Bahamas and E. jarocho from the Veracruz area of the Gulf of Mexico.
Adult cleaner gobies are separated mostly by color patterns and the shape of the snout. Some have a distinctly underslung upper jaw, the true "sharknose" appearance (E. evelynae, E. genie, E. illecebrosus, and E. oceanops), but this character can be indistinct on larvae and recruits. Color patterns on adults, yellow vs. white vs. blue, are important characters but also may be inconsistent on recruits. In general, the most useful patterns for distinguishing new recruits are the various markings on the snout.
