Small species without commercial value are often overlooked in conservation management. Pygmy perches are minature percichthyid fishes from temperate southern Australia of significant conservation concern, with five of the seven described species being threatened nationally. The present paper examines the plight of Yarra pygmy perch Nannoperca obscura, and variegated pygmy perch N. variegata, and discusses the progress of national (and State) recovery-plan actions. Threats and risks to these species are considerable; however, overall, few recovery actions have been completed and the status of many populations is unknown following the recent ‘millenium drought’. Habitat restoration, fish rescues, environmental water delivery and research into distribution, ecology and population dynamics are largely driven by individuals within singular local management authorities. Like many small fishes, they receive less attention than do larger ones and a cross-jurisdictional national recovery team is required to prioritise, coordinate and implement conservation efforts before the continued persistence of these species can be assured. These two small fishes are representative of many similar species and the lessons from the present case study may be applied elsewhere throughout the world.