The low cost and infinite lifetime of Passively Integrated Transponder (PIT) tags makes them a popular choice in fisheries management. Recent advances in PIT technology have meant smaller tags can now be used to mark smaller-bodied fishes, many of which are threatened. The suitability of 9 mm PIT tags for identification of threatened small bodied galaxiids was tested in an aquaria trial using Mountain Galaxias Galaxias olidus as a surrogate, with tags inserted into the abdominal cavity. Fish down to 73 mm LCF were tagged, and no significant difference in growth or survival was detected between control and tagged fish (n_control = 34, n_tagged = 34) after 90 days. Tag retention rate was high (96%), with only a single tag expelled. Following the aquaria trial, 38 critically endangered Stocky Galaxias G. tantangara were tagged to investigate individual movement in Tantangara Creek. Fish were monitored using a portable PIT antenna for six months between January and June 2018. Preliminary findings indicate G. tantangara exhibits a small home range (< 20 lineal metres) but can undergo larger up and downstream movements. PIT tag biomonitoring is likely a valuable tool in the management of other small bodied threatened fishes, especially other Australian galaxiids.