The diatom Didymosphenia geminata, which forms nuisance blooms in low nutrient streams worldwide, was documented as an aggressive invader in South America in 2010 from the Futaleufú basin (43.2°S), in Chilean and Argentinean Patagonia. Within 1 year it was confirmed from 20 rivers distributed over 800 km. Driven by perceived economic impacts to tourism and recreation, a strong response ensued, with education, monitoring and nascent biosecurity efforts based on similar measures in New Zealand. Considering the difficulty in containment (potential range on New Zealand's South Island was occupied by D. geminata within 3 years), the much larger potential range, and limited resources or previous experience in managing invaders in continental waters in South America, it is unlikely that current biosecurity measures will produce significant results. Lacking a coordinated strategic approach or conservation priorities, existing efforts may divert resources from alternatives with greater potential for success, while potentially feeding the public perception that the problem is being addressed. We propose a conservation strategy based on best available but incomplete information on habitat requirements, and a conceptual model of invasion vectors to identify defensible conservation zones (islands and hydrographically isolated areas) with greater potential for being maintained invasion-free.