Manganese import, transport, accumulation, sensing and control pathways are important for all organisms, and of unique importance for oxygenic photosynthetic organisms due to their role in the catalysis of water oxidation by photosystem II (PSII) complexes. In this review we will describe the general aspects of Mn biochemistry, its known roles in cellular processes and its mode of function in PSII. We will describe in detail different chemical mechanisms that have evolved to obtain and control Mn ions, especially focusing on cyanobacterial systems as an example of organisms with absolute Mn requirements that populate a wide variety of environments. We will describe the steps and mechanisms by which Mn transport is performed under Mn deficient or replete conditions. Under deficient conditions a high affinity Mn transporter is expressed and becomes functional in the cyanobacterial plasma membrane. This ATP dependent transporter must overcome a number of mechanistic problems to perform its function: bind Mn ions with high affinity and specificity at very low Mn concentrations in the possible presence of higher concentrations of similar metal ions. The Mn cluster of PSII functions within the cyanobacterial cell, yet studies suggest that it is assembled in the plasma membrane facing the periplasmic space rather than in the thylakoid membrane. The topology of the two processes, Mn transport and Mn cluster assembly, should therefore be regulated in order to insure efficient biogenesis and repair of PSII complexes. Based on the available results, we attempt to map the constraints imposed by Mn transport on PSII biogenesis events in cyanobacteria.