Preparative isoelectric focusing was employed to compare the association of protochlorophyllide and chlorophyllide with the enzyme NADPH‐protochlorophyllide oxidoreductase (PCR; EC 1.3.1.33). Photoactive protochlorophyllide‐PCR complexes were solubilized with 1‐O‐n‐octyl‐β‐d‐glucopyranoside from non‐irradiated prolamellar bodies of wheat (Triticum aestivum). Also, chlorophyllide‐PCR complexes were solubilized from prolamellar bodies irradiated under conditions either preventing or favouring a spectral shift of chlorophyllide to shorter wavelengths. Independently of the treatment prior to the solubilization, the pigments and the PCR focused together at pHs of 4 to 5. The results indicate that protochlorophyllide‐PCR complexes are conformationally similar to chlorophyllide‐PCR complexes. The results support the hypothesis that the spectral shift, referred to as the Shibata shift, reflects a breaking‐up of large chlorophyllide‐PCR aggregates to smaller chlorophyllide‐PCR units, rather than a dissociation of the chlorophyllide from the enzyme protein.