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Emerging DNA sequencing technologies are making it quicker, cheaper, and easier to generate massive sequence data from environmental samples. This deluge of information can quickly overwhelm our capacity to interpret results, understand how fungal communities are structured, and identify keystone species. In this talk I will provide a perspective based on my research in natural ecosystems and based on studies of fungi that are not well represented in sequence databases. I will discuss how the new, enhanced sequencing capacity ironically increases our reliance on reference databases and therefore necessitates more molecular systematic studies of fungi as well as widespread sequencing directly from fungal herbaria and culture collections. I will also discuss the importance of phylogenetically-focused sampling and how combinations of molecular and non-molecular approaches could be used to enhance our understanding ofe nvironmental sequences. I will argue that fungal systematics and ecology are inextricably linked and that both are necessary to adequately comprehend the ever-expanding flood of new sequences.<p><p>Keywords: