Secondary compounds leached from plant litter can negatively affect aquatic amphibian larvae. Non-native plants and their potentially distinct secondary compounds may constitute cryptic threats to native amphibians. We used the availability of both native and introduced Phragmites australis (common reed) populations in North America to assess the importance of origin, intraspecific variation, and two purified classes of compounds (tannins and saponins; gradients 0-25 mg L(-1)) on two common and widespread amphibians (Ambystoma maculatum, spotted salamander, and Lithobates palustris, pickerel frog). In experiments with purified compounds, high tannin concentrations reduced A. maculatum survival and developmental rate while high saponin concentrations reduced survival, developmental rate, and size of L. palustris and reduced A. maculatum developmental rate. In experiments using leaf litter extracts of 14 different P. australis populations, A. maculatum larval survival varied among populations but plant origin (native or introduced) did not explain this variation. In contrast to the lack of effects of purified saponins, increases in saponin concentrations in P. australis leachates significantly decreased A. maculatum survival. Our results suggest: (1) secondary compounds can impact larval amphibian survival and development in species-specific ways; (2) impacts of P. australis on A. maculatum vary among P. australis populations, reflecting intraspecific variation in secondary chemistry; and (3) origin (whether the plant is native or introduced) is a poor predictor of P. australis effects on A. maculatum. Scientists and managers may need to move beyond considering origin as a predictive variable when managing plant communities to benefit amphibians.