A noncovalently bound, ordered complex consisting of fragments (1-25)H and (14-103) derived from tuna cytochrome c has been prepared and characterized. The equilibrium properties of this complex are indistinguishable from those of the corresponding complex, (1-25)H X (23-104), of horse cytochrome c. The tuna species possesses a second tryptophan residue (at position 33 of the amino acid sequence and replacing the histidine residue of the horse protein) whose fluorescence is also essentially fully quenched in the native form and in the complex. It is found that for the tuna complex, the fluorescence of both tryptophans is fully quenched during the second order phase of the reaction mechanism. This provides evidence for the compact nature of the intermediate complexes formed at this stage of the complementation process (Parr, G. R., and Taniuchi, H. (1982) J. Biol. Chem. 257, 10103-10111). The observed second order rate constant for the tuna fragments is reduced by a factor of two from that for the horse fragments. During the first order kinetic phase corresponding to the transition from the intermediate complexes to the native complex, qualitative as well as quantitative differences are also observed between the tuna and the horse species. The kinetics of complementation of the "hybrid" complexes is also reported. This exchangeability of both the heme fragment and the apofragment of the complex between these two species indicates close similarity of the folding mechanism. Nonetheless, the results also serve to highlight the subtle effects exerted on the folding process by a relatively small number of changes (17%) in the amino acid sequence.