It has previously been shown that the "partial" reaction between fatty acyl-CoA dehydrogenase and acyl-CoA substrate is pH-dependent (larger rate constants at basic pH) and shows a biphasic rate profile indicative of formation of an initial charge transfer complex between the C-2 anion of substrate and enzyme. The present investigation indicates that the complete reaction between acyl-CoA and electron transfer flavoprotein shows a pH profile dependent upon ionization of a single basic group with pKa = 7.7. these facts are consistent with electron transfer which occurs through an obligatory charge transfer complex between the C-2 anion of substrate and oxidized FAD at the enzyme active site. The anion of acetoacetyl-CoA forms a charge transfer complex with enzyme which serves as a model for the putative catalytically active complex mentioned above. Resonance Raman investigation of this acetoacetyl-CoA-enzyme complex indicates that the 1586 cm-1 band is coupled strongly to the charge transfer electronic transition. Since this vibrational band is associated with vC=N at N-5, C-4a of the flavin ring, we suggest that electron transfer takes place at this site.