In contrast to the majority of cyanobacteria, the unicellular marine cyanobacterium Prochlorococcus marinus MED4 uses an intrinsic divinyl-chlorophyll-dependent light-harvesting system for photosynthesis. Despite the absence of phycobilisomes, this high-light adapted strain possesses -phycoerythrin (CpeB), an S-type lyase (CpeS), and enzymes for the biosynthesis of phycoerythrobilin (PEB) and phycocyanobilin. Of all linear tetrapyrroles synthesized by Prochlorococcus including their 3Z-and 3E-isomers, CpeS binds both isomers of PEB and its biosynthetic precursor 15,16-dihydrobiliverdin (DHBV). However, dimerization of CpeS is independent of bilins, which are tightly bound in a complex at a ratio of 1:1. Although bilin binding by CpeS is fast, transfer to CpeB is rather slow. CpeS is able to attach 3E-PEB and 3Z-PEB to dimeric CpeB but not DHBV. CpeS transfer of 3Z-PEB exclusively yields correctly bound Cys 82 -PEB, whereas Cys 82 -DHBV is a side product of 3E-PEB transfer. Spontaneous 3E-and 3Z-PEB addition to CpeB is faulty, and products are in both cases Cys 82 -DHBV and likely a PEB bound at Cys 82 in a non-native configuration. Our data indicate that CpeS is specific for 3Z-PEB transfer to Cys 82 of phycoerythrin and essential for the correct configuration of the attachment product.