Single-crystalline photochromism of 1,2-bis(2-methyl-5-phenyl-3-thienyl)perfluorocyclopentene 1a was followed in situ by X-ray crystallographic analysis. The crystal of 1a has two molecules with different conformations in the crystallographic asymmetric unit. The X-ray analysis of the photoirradiated crystal showed that the photocyclization reaction of the molecule with the shorter distance between the reactive carbons prevails over the reaction of the other molecule. The mechanism has been discussed based on the calculation of the electronic transitions of the two molecules in the different conformations. The photocyclization quantum yield was determined to be 1 (100%) in the crystal.