An extensive superfamily of cupins (clan cl09118) currently combines thousands of functionally and structurally diverse prokaryote and eukaryote proteins, which contain a beta-barrel of antiparallel beta-strands (cupin module). Possible ways of the formation of the cupin superfamily were suggested based on the comparison of primary and tertiary structures of proteins from several conserved families of cupins including seed storage globulins and plant oxalate oxydases (germins), and bacterial oxalate decarboxylases, gentisate dioxygenases and epimerases. The origin of two-domain structure of seed storage globulins from cyanobacterial two-domain oxalate decarboxylases has been deduced. The evolutionary pathway of single-domain germins previously suggested to be immediate progenitors of storage globulins was traced back. Common evolutionary roots of germins and oxalate decarboxylases descend from recent bacterial and archaebacterial proteins whose primitive structure is restricted to the cupin module. These root proteins reflect the hypothetical structure of a pro-cupin that probably gave rise to at least a part of the total diversity of members of the cupin superfamily (for instance, to the cupin module of gentisate dioxygenases). The major dilemma for the description of the cupin superfamily is distinguishing evolutionary divergence from convergence. The structural convergence can be exemplified by formation of a beta-barrel inside extremely conserved structures of the otherwise unrelated epimerases from Archaea and bacteria.