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Recent phylogenomic studies revealed a robust and new hypothesis explaining annelid phylogeny. Most surprising was the existence of a few basal lineages showing a comparatively simple organization. In view of this new phylogeny the evolution of organ systems in annelids and the characters probably present in their last common ancestor have to be reevaluated. With respect to the light sensitive organs a pair of simple larval eyes and two pairs of adult eyes is regarded as being present in their last common ancestor. Typically adult eyes are multicellular pigment cup or pinhole eyes applying rhabdomeric photoreceptor cells (PRCs) and pigmented supportive cells (PSCs) in converse design. However, in the most basal lineages eyes are only present in a limited number of taxa and thus far their structure was unknown. Ultrastructural investigations in members of these lineages, Oweniidae and Chaetopteridae, revealed a completely different but corresponding structure of eyes and PRCs shedding new light on the evolutionary history of adult eyes in Annelida. The eyes in species of this basal radiation are simple pigment spot eyes and part of the epidermal epithelium comprising two cell types, monociliated PSCs and rhabdomeric PRCs. Both cell types show characteristics typical of epidermal supportive cells. These findings indicate that the annelid stem species most likely possessed a pair of pigment spot eyes with slightly specialized PRCs and, as is the case for the nuchal organs, pigment cup adult eyes presumably evolved later in annelid phylogeny, namely in the stem lineage of Amphinomida and Pleistoannelida.