Animals that occupy holes or squeeze into interstitial spaces often have particularly flexible bodies and can be difficult to tag effectively. The present study evaluated three methods for radio-tagging the cryptic, eel-like fish Gadopsis bispinosus, a species that inhabits interstitial spaces among cobbles and boulders in streams. The three methods were an externally attached radio-tag with a whip antenna, an internally implanted coil radio-tag (internal coil) and an internally implanted radio-tag with an externally exited whip antenna (internal-external). Successful radio-tagging was determined in aquaria trials based on a combination of four indicators: (1) survival; (2) retention of the radio-tag; (3) healing of the surgical incision; and (4) rapid resumption of feeding. Externally attached radio-tags were shed and proved to be unsuitable (100%). Three of nine individuals with internal-external tagging completed the study with regular feeding, healed incisions and retained radio-tags. Conversely, five of nine individuals with internal coils were successful. This included two of three individuals held in either a simple environment for 3 days or for the duration of the trial and one of three individuals held in a complex environment. Temporary confinement following implantation with coil radio-tags offers a viable means of radio-tagging G. bispinosus. Temporary confinement following radio-tagging may also be useful for reducing radio-tag rejection and mortality for other fish species with similar body morphs and habitat use (e.g. eel species and sculpin).