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The longnose darter Percina nasuta is a rare and cryptic fish that recently disappeared from much of its historic range. We developed and used an environmental DNA (eDNA) assay for longnose darter paired with visual surveys to better determine the species' range and compare detection probability between sampling approaches in an occupancy modeling framework. We detected longnose darter eDNA further upstream in the mainstem St. Francis River than previously reported and in a tributary for the first time. Our multi-scale occupancy approach compared models where detection was constant against a model that allowed detection to vary by survey method. The constant model received the most support indicating survey method was not a strong predictor and detection was estimated at 0.70 (0.45–0.86; 95% CI) across both methods. Our study produced effective longnose darter eDNA primers and demonstrated the application of eDNA for sampling small-bodied, cryptic fish. We detected longnose darter eDNA 27 km upstream of their known range and determined that snorkel surveys are the most efficient sampling method if water clarity allows. We recommend target sample sizes to achieve various detection goals for both sample methods and our results inform future design of distributional and monitoring efforts. [ABSTRACT FROM AUTHOR]