Marine species live out-of-sight, consequently geographic range, population size and long-term trends are extremely difficult to characterise for accurate conservation status assessments. Detection challenges have precluded listing of marine bony fishes as Extinct on the International Union for Conservation of Nature (IUCN) Red List, until now (March 2020). Our data compilation on handfishes (Family Brachionichthyidae) revealed them as the most threatened marine bony fish family, with 7 of 14 species recently listed as Critically Endangered or Endangered. The family also includes the only exclusively marine bony fish to be recognised as Extinct – the Smooth handfish (Sympterichthys unipennis). Ironically, some of the characteristics that threaten handfishes with extinction have assisted assessments. Poor dispersal capabilities leading to small, fragmented populations allow monitoring and population size estimation for some shallow water species. Evidence that the Smooth handfish is now Extinct included no sightings over 200 years in an area subject to numerous scientific surveys, inferred shallow habitat and moderate abundance at time of original collection, and major habitat transformation through fishing, aquaculture, rising sea temperature, and urban development. Contemporary threats to extant handfish species include habitat degradation, introduced species, loss of spawning substrate, climate change, and demographic risks associated with small, fragmented populations. Multifaceted conservation efforts are needed, including addressing threats to habitat quality, bolstering wild population numbers, and implementing novel techniques to find and monitor populations. Expanded monitoring, including application of eDNA methods, represent critical steps towards overcoming the challenges in studying wild populations of rare marine species. Ongoing investigation will likely reveal numerous other threatened species for which little is known.