Hybridization between Saltmarsh Sparrow (Ammodramus caudacutus) and Nelson's Sparrow (A. nelsoni) has been documented in areas where the two species occur sympatrically, increasing the difficulty of accurate species identification. We developed a DNA barcoding restriction fragment length polymorphism (RFLP) test to discriminate between Nelson's Sparrows and Saltmarsh Sparrows and applied it to 426 putative Saltmarsh Sparrows sampled from Maine to New York, USA. All individuals were identified in the field as Saltmarsh Sparrows based on morphology, but 34 (8%) had Nelson's specific mitochondrial DNA, indicating they were of hybrid origin. This discrepancy in morphological and genetic data highlights the difficulties associated with accurate field identification and may hinder conservation efforts by confounding attempts to identify and monitor “pure” populations. Mitochondrial DNA of Nelson's Sparrow was prevalent at the most southern point of the previously documented overlap zone and was also found in one individual 150 km south of the overlap zone. Our findings offer new insights into the extent of hybridization between the two species and underscore the need for further investigation into the consequences of hybridization on conservation of Saltmarsh Sparrows.