More than 15 years ago, on the basis of phylogenetic analyses of a handful of anciently duplicated genes and of rRNA, Carl Woese proposed both a eubacterial rooting of the Tree of Life and a stepwise evolution of the eukaryotic cell. An important part of Woese's paradigm was the assumption that the so-called Archezoa were considered to be genuinely primitive because they were lacking mitochondria and several other organelles characteristic for most eukaryotes. Since then, enormous progress have been accomplished in sequencing technology and in phylogenetic reconstruction. In particular, it is now clear that a tree reconstruction artefact, known as Long Branch Attraction, is responsible for the early emergence of the fast evolving Archezoa in the eukaryotic tree. The corollary hypothesis that all extant eukaryotes are ancestrally mitochondrial is strongly supported by the discovery of rudimentary mitochondrial organelles in all analysed Archezoa. Today a consensus that divides the extant eukaryotes into six major groups is replacing Woese's paradigm, which needs, however, further confirmation. Recently, a molecular dating study based on a large phylogenomic dataset with a relaxed molecular clock and multiple time intervals yielded in a surprisingly recent time estimate of 1085 Mya for the origin of the extant eukaryotic diversity. Therefore, extant eukaryotes seem to be the product of a massive radiation that happened rather late, at least in terms of prokaryotic diversity. In multiple cases evolution has proceeded via secondary simplification of a complex ancestor, instead of the constant march towards rising complexity generally assumed. Therefore it is time to reevaluate the origin and evolution of eukaryotes, in light of the newly established phylogeny, by further integrating secondary simplification as an equal partner to complexification.