Planctomycetes and some related species are unique among the domain Bacteria in possessing cells with a complex plan defined by internal membranes forming separated compartments within the cell. They also possess other unique features such as cell walls composed of protein as a major polymer instead of the peptidoglycan typical of other Bacteria. All species examined display an underlying shared cell organization in which an internal intracytoplasmic membrane separates two major cell compartments, an outer ribosome-free paryphoplasm and a more central ribosome-containing pirellulosome. Some planctomycete species have three compartments, where further membranes within the pirellulosome define another compartment, the anammoxosome in anammox planctomycetes and the membrane-bounded nuclear body in Gemmata obscuriglobus. Functional features which are correlated with structural compartmentalization in planctomycetes include in G. obscuriglobus the ability to take up proteins within the paryphoplasm of the cell by a mechanism similar to receptor-mediated endocytosis of eukaryotes, and in anammox planctomycetes such as Kuenenia stuttgartiensis, anaerobic ammonium oxidation. The anammoxosome compartment is central to the biochemistry performed by anammmox planctomycetes, important contributors to the global nitrogen cycle and to wastewater remediation at industrial scale.  Planctomycetes will be increasingly important for progress in both fundamental and applied microbiology.