INDO/2 studies have been carried out for the elucidation of the relative environment of the plastoquinones Q(I) and Q(II) in thylakoid discs in chloroplast. The corresponding quinones in bacteria are Q(A) and Q(B), which are known to be plastoquinones, menaquinones, or ubiquinones. We show that a major part of the free energy of reduction of Q(II) by Q(I) (-0.13 eV in vivo) can be accounted for if the plastoquinone of Q(I) contains, in lieu of one of the methyl substituents, a side chain like -NHR or -NHCOR which serves as a link to the protein moiety in the photosynthetic unit (PSU). Here R represents an alkyl group. Chains like -NRR’ and -NRCOR’ are also possible substituents of Q(I). The remaining part of the free energy of reduction can be attributed to a slight difference in the polarizable environment not directly bonded to the plastoquinones.