The rapidly growing use of eDNA-based detection for low-abundance species requires well-designed protocols to improve sensitivity. Knowledge of the limits of eDNA technology is imperative, particularly when applied to conservation biogeography studies for detecting non-indigenous or endangered species. Our results highlight the currently inadequate sensitivity screening of genetic markers used in most studies, contrasting the transition to highly sensitive PCR methods. Along with ongoing calls for standardization in the eDNA methods, we add that newly-designed markers be screened to determine and optimize sensitivity before use to reduce the uncertainty of detection and benefit future applications within or beyond areas of their development.