Coral reefs, one of the most biologically diverse and important ecosystems on Earth, are experiencing unprecedented and increasing ecological decline, yet the fish faunas of such reefs and other tropical shoreline habitats remain poorly known in many areas. Rotenone, a natural substance traditionally used by subsistence fishers, is a uniquely efficient tool for sampling reef and other shore fishes for marine research. Unfortunately, such sampling is perceived as being highly destructive, and increasing prohibitions against using rotenone in many countries will soon cripple essential research on reef-fish biodiversity worldwide. In this article we dispel common misconceptions about the environmental effects of small-scale rotenone sampling in marine research.