Passive Integrated Transponder (PIT) telemetry has recently been adapted for locating PIT-tagged fish in shallow waters using portable detectors. In the present study, we tested this method for adult amphibians (Pyrenean brook salamanders, Calotriton asper) PIT-tagged with 12-mm transponders in a headwater rocky stream. PIT telemetry performances were compared with a conventional hand-capture method, i.e. visual searching and overturning movable stones in the streambed. The mean efficiency of the portable detector (88.2% ± 5.2, s.e.) was significantly higher than hand-capture (51.1% ± 6.4) and the operator progressed, on average, four times faster. Time efficiencies were, on average, 0.92 (±0.15) and 0.12 (±0.04) adult salamanders per minute with the portable detector and by hand-capture, respectively. The efficiency of the portable detector was negatively correlated with the percentage of large stones on the streambed. The time needed to prospect a section was positively correlated with the abundance of PIT-tagged adult salamanders, spring inlets and undercut banks. Because PIT telemetry is less disruptive than hand-capture for both salamanders and their habitat, it is a promising and non-disruptive method for developing studies on the ecology and management of amphibians in shallow waters.