Amphidromous stream-cling-gobies of the genus Stiphodon comprise an important component of the fish communities in insular streams of tropical Indo-Pacific high islands. We aimed to develop an effective and rapid method of surveying Stiphodon atratus in a continental stream and then apply the method in an untested stream. Triple-pass snorkelling of a single pool revealed the reliability of single-pass estimates of the abundance of S. atratus. Single-pass survey of a reach in each of two streams then confirmed the presence of S. atratus, Stiphodon semoni and Stiphodon rutilaureus, in Australia. However, Stiphodon were in low abundance (S. atratus, Cooper Creek, n = 38, Pauls Pocket Creek, n = 45; S. semoni, Cooper Creek, n = 4, Pauls Pocket Creek, n = 14; S. rutilaureus, Cooper Creek, n = 0, Pauls Pocket Creek, n = 38). Preliminary indications are that particular streams provide critical habitat for newly discovered assemblages of Stiphodon within the Australian Wet Tropics. Small population sizes, coupled with the attractiveness of Stiphodon as aquarium pets, warrants that national protective status is provided to this genus until a comprehensive understanding of species distribution, abundance and population genetic structure is achieved.