The Paleoproterozoic (2.5-1.6 Ga) Era is a decisive time in Earth and life history. The paleobiological record (microfossils, stromatolites, biomarkers and isotopes) illustrates the biosphere evolution during a time of transitional oceanic and atmosphere chemistries. Benthic microfossil assemblages are recorded in a variety of oxygenated, sulfidic, and ferruginous environments representative of the spatial heterogeneities and temporal variations characteristic of this Era. The microfossil assemblages include iron-metabolizing and/or iron-tolerant prokaryotes, sulfur-metabolizing prokaryotes, cyanobacteria, other undetermined prokaryotes, and eukaryotes. The undetermined microfossils represent a majority of the assemblages and thus raise a challenge to determine the nature and role of microorganisms in these changing environments. Despite the early evolution of the eukaryotic cellular toolkit, early eukaryotic crown group diversification may have been restrained in the Paleoproterozoic by ocean chemistry conditions, but it increased during the late Mesoproterozoic-early Neoproterozoic despite the continuation of similar conditions through the (miscalled) "boring billion", then amplified significantly (but perhaps within lower taxonomic levels), with the demise of euxinic conditions and increase in ecological complexity. The emerging picture is one of a changing and more complex biosphere in which the three domains of life, Archaea, Bacteria and Eukarya, were diversifying in various ecological niches marked by the diversification of identified microfossils, stromatolites, increasing abundance of preserved biomarkers, and appearance of macroscopic problematic fossils or trace fossils.