Photoinduced electron transfer (PET) between s e l f -a s s e m b l e d t r a n s -or c i s -i s o m e r o f 4 , 4 ′ -s t i l b e n e d i c a r b o x y l i c a c i d ( S D B A ) a n d [ N , N ′ -di(2-(trimethylammoniumiodide)ethylene)]perylenediimide(PDI-I) in water has been investigated. Both trans-SDBA and cis-SDBA molecules can form stable complexes with columnar PDI-I aggregates in water with a 1:1 stoichiometry via ionic interactions, but the complex of cis-isomer is more stable as revealed by the UV-vis absorption and fluorescence spectroscopy. The electrochemical experiments suggest that cis-SDBA is a better electron donor than its trans-isomer. However, fluorescence quenching experiments suggest that the electron transfer from trans-SDBA is more efficient than that from cis-SDBA, which is obviously contradictory to the results of binding constant and the electrochemical experiments. The contradictory results can be attributed to that the columnar aggregates (PDI-I) n are utterly destroyed in cis-SDBA-(PDI-I) n system caused by stronger ionic interaction between cis-SDBA and (PDI-I) n . Also, the bending conformation of cis-SDBA probably results in a larger distance between cis-SDBA and the surface of (PDI-I) n . The results of this research suggest that the electron transfer can be tuned by the aggregation and/or configuration of the donors and acceptors.