PixD/Slr1694 from the cyanobacterium Synechocystis sp. PCC6803 is a member of a new class of flavin-containing blue-light sensory proteins containing a BLUF (blue light using flavin) domain. The photocycle reaction mechanism of BLUF is unique because only small structural changes of a bound chromophore are accompanied by a few hydrogen bond rearrangements in the chromophore-binding site. Here, we show that in PixD, Met93, the residue conserved in all BLUF domains, is crucial for light-dependent signal transduction. Specifically, the light-insensitive M93A mutant of PixD revealed biochemical and physiological activities compatible with those of the light-adapted wild-type PixD. However, the W91A mutant of PixD retained light sensitivity and biological function, although the corresponding mutant of another BLUF protein, AppA, has been reported to be locked in the light signaling state. These observations suggest that the pathway through which the light signal is transformed into apoprotein structural changes has been modified in BLUF proteins for their respective functions.