The order Anguilliformes (true eels) consists of around 1000 species worldwide in 16 different families, numbers that are comparable to other highly diverse groups such as sharks and rays. In Australia, over 200 eel species in 13 families are represented from freshwater, estuarine and shelf waters to the edge of the continental slope and abyssal plain beyond 3000 m depth. As adults, species occupy a variety of habitats from within benthic sediments and caves to benthopelagic and mesopelagic zones in tropical to polar waters. Although freshwater eels (Anguillidae) have received considerable attention worldwide due to their commercial importance, most marine eels are poorly studied despite their ecological importance and sometimes high abundances, as evident from trawl catches and underwater video. The poorly-sampled cryptic habitats often occupied by eels have confounded the understanding of their taxonomy and biology as many species are only known from a handful of specimens. On occasions, species were described based on their leptocephalus larval stage, their corresponding adult forms yet to be determined. Opportunistic data collection during regional faunal surveys, examination of museum fish collections over a 15 year period and molecular techniques (DNA barcoding) have all helped revise alpha-taxonomy to reveal numerous cryptic and previously unrecognised species. Structure of the Australian marine eel fauna is discussed within different taxonomic groupings, habitats and bioregions. Comparisons to other regional faunas in the Indo-Pacific show varying levels of endemicity, and is highest in the Congridae and Ophichthidae. Families covered in most detail include the Congridae (conger eels), Muraenidae (moray eels) and Synaphobranchidae (basketwork eels).