ABSTRACT1. Traditionally headwater streams are surveyed using electrofishing, a potentially harmful sampling method. Increasingly scientists are seeking out the least destructive stream sampling methods, especially when sampling imperilled fishes. It is therefore imperative that the efficacy of alternative, non-destructive sampling methods be investigated.2. This study investigated the potential for using underwater video analysis (UWVA) as an alternative to electrofishing for assessing the diversity and relative abundance of imperilled fishes in clear, relatively shallow (<1.5 m) headwater streams.3. Detection rates using UWVA were higher than with electrofishing, relative abundance estimates between the two methods were significantly correlated, the attractive effect of the camera was negligible and UWVA was logistically feasible for sampling small headwater streams.4. These results have clear conservation implications as it was demonstrated that UWVA is a suitable sampling method for estimating relative abundance of fishes in small, clear headwater streams.