Phycobilisomes are the major light harvesting complexes in photosynthesis. Two types of phycobilisomes exist: the large PBS consisting of a core and rods (herein PBS) and the rod-only CpcL-PBS, which contains a membrane-attaching linker CpcL. PBS that are mainly associated with PSII and CpcL-PBS are mainly associated with PSI. We here report (1) the Cryo-EM structure of PBS from Synechococcus sp. PCC 7942, which contains a two-cylinder core and six rods. The bundle-shaped PBS structure of Gloeobacter 7421 was also determined with Cryo-Em combined with mutagenesis analysis. (2) We compare how rods are attached to the cores in different cyanobacterial PBS, which are crucial to the functions of PBS. (3) The roles of linker proteins as well as phycobiliproteins in energy transfer in PBS. (4) The attachment of PBS to PSII is studied and we show here that a small linker protein (Linker for PBS-PSII, Lpp72) is required for such an attachment in the cyanobacterium Synechococcus PCC 7002. In the absence of the gene encoding Lpp72, Synechococcus 7002 grew much more slowly under a green light illumination. Oxygen evolution rate in the lpp72 mutant illuminated with a 590-nm light was greatly reduced. We demonstrate that Lpp72 interacts with both CP47 of PSII and ApcB of PBS.