Biodiversity assessment underpins our understanding of ecosystems and determines environmental management decisions on resource use and conservation priorities. Recently, a new discipline - environmental or ecological genomics (ecogenomics) - has emerged from major advances in sequencing technologies, such as pyrosequencing (a technique based on the detection of pyrophosphate during nucleotide incorporation), and enabled extraordinary progress in the way biodiversity can be assessed. Since 2008, numerous highimpact microbial metagenomic sequencing studies, which have relied on both classical and next-generation sequencing, have been published. As a result, many previously unrecognized taxa and biota have been identified, but none of these studies explored eukaryote diversity. Here, we illustrate the power of applying nextgeneration pyrosequencing to identify and enumerate eukaryote species assemblages in the context of assessing the impacts of human activity on ecosystems.