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Aim Establishing the distribution and diversity of populations in the early stages of invasion when populations are at low abundance is a core challenge for conservation biologists. Recently, genetic monitoring for environmental DNA (e DNA) has become an effective approach for the early detection of invaders, especially for microscopic organisms where visual detection is challenging. Didymosphenia geminata is a globally distributed freshwater diatom that shows a recent emergence of nuisance blooms, but whose native versus exotic status in different areas has been debated. We address the hypothesis that the distribution and genetic diversity of D. geminata in eastern North America is related to the recent introduction of non-native lineages, and contrast that with the alternative hypothesis that D. geminata is cryptically native to the region (i.e. at low abundance) and only forms nuisance blooms when triggered by a change in environment. Location The Mid-Atlantic region of North America. Methods We analysed 118 stream samples for D. geminata e DNA, validated our results for a subset of sites using direct visual enumeration by microscopy and used molecular cloning to sequence D. geminata from two sites where e DNA was detected. Results (1) D. geminata e DNA was detected at seven spatially unique sites, six of which were previously documented to contain recent D. geminata blooms. (2) Sites where D. geminata e DNA was detected exhibited no difference in environmental conditions compared to sites with no-detected D. geminata e DNA. (3) Sequencing of D. geminata e DNA showed that blooms were composed of multiple genetic lineages, closely related to those sampled elsewhere across the globe. Main conclusions We interpret these results as most consistent with the hypothesis that D. geminata is an exotic invader in the Mid-Atlantic region, still in its early stages of invasion; thus, genetic monitoring and management efforts may still be effective at controlling its spread. [ABSTRACT FROM AUTHOR]