We systematically studied the visual spectral changes of short-chain, medium-chain, and long-chain acyl coenzyme A (acyl-CoA) dehydrogenases, purified from rat liver mitochondria, that occur upon reaction with acyl-CoA in the absence of an electron acceptor (half-reaction). Acyl-CoA esters having various chain lengths were tested, and changes in the steady-state spectral parameters were correlated with the turnover number in the complete reaction, which represented the ability of an enzyme/substrate combination to produce an enoyl-CoA. The long-wavelength absorbance, centered around 580 nm, was observed only in the enzyme/substrate combinations in which enoyl-CoA product was produced at a significant rate in the complete reaction. There was a good correlation between the magnitudes of the long-wavelength absorbance and the turnover numbers. In contrast, the bleaching of the flavin chromophore at 450 nm was observed not only in the titration with preferred substrates but also in that with unfavorable substrates, which were shorter than favorable substrates. In the interaction with the shorter than favorable substrates, however, enoyl-CoA was not produced, nor did long-wavelength absorbance occur. When short-chain and medium-chain acyl-CoA dehydrogenases were reacted with longer than favorable substrate from which no enoyl-CoA was produced, neither the appearance of the long-wavelength absorbance nor bleaching of flavin chromophore was observed. These data suggest that the catalytic base, which abstracts alpha-proton, and flavin adenine dinucleotide are internally located, and the region containing these two sites may physically be in the form of crevice or pocket.