<p>Molecular omics methods are dramatically transforming the field of ecology, allowing research questions and hypotheses to be tested in situ that would have been impossible to answer just a few years ago. A frequently neglected component of terrestrial habitats are microalgae and cyanobacteria, which are found almost everywhere on Earth, from the cold deserts of the polar regions to tropical rainforests and from endolithic species to epiphytic forms growing on trees and free-living and symbiotic forms, and are often important primary producers in their respective ecosystems. Although significant progress has been made in recent years, our understanding of the biodiversity (intra- and interspecific) of these organisms remains limited, particularly with regard to their ability to withstand the extreme conditions of their specific habitats. In this report we explore the potential of omics methods to advance the analysis and facilitate a more comprehensive understanding of these fascinating organisms.</p>