In a cyanobacterium, Synechococcus elongatus PCC 7942, a circadian input protein Pex accumulates in dark transiently, and then down-regulates the transcription of the clock gene kaiA. Herein, we analyzed molecular size of a protein complex of Pex in vivo. The extract of the cyanobacterial cells were fractionated. Then, Pex in the obtained fractions were examined by western blotting method. A protein band in 17 kDa was detected as Pex protein in 34 kDa complex, in addition to previously reported 13 kDa protein in 17 kDa complex. The 17 kDa protein signal was absent in pex deficient mutant cell extract, therefore we determined the 17 kDa protein was Pex. The size of 17 kDa is consistent to the one deduced from the open reading frame of pex. We also present significance of hydrophobic amino acids important for the dimer formation of Pex.