We evaluated the feasibility of using passive integrated transponder (PIT) tags to mark and track individual shorthead sculpins (Coitus confusus). We implanted PIT tags in 80 shorthead sculpins in 2 size categories (60–80 mm and 81-106 mm total length) and in 1 of 2 locations (subcutaneous along the spinous dorsal fin or in the body cavity). We evaluated tag retention, sculpin survival, and net-avoidance behavior for 29 days. We observed no mortality directly attributable to PIT-tag injection at either tagging location. We observed a 38.8% loss rate of dorsal tags and a 2.5% loss rate of body-cavity tags. No change in net-avoidance behavior was observed. We released 97 PIT-tagged sculpins into an artificial stream and monitored them with 3 stationary and 1 portable antenna. Sixty sculpins were detected at least once, and 18 sculpins were detected multiple times with the portable antenna. These results indicate that PIT-tagging within the body cavity is a feasible method for marking and tracking individual shorthead sculpins.