By using single molecule fluorescence resonance energy transfer (smFRET), the equilibrium denaturation of staphylococcal nuclease (SNase) induced by guanidinium hydrochloride (GdmCl) has been investigated. We have characterized the collapse of the denatured chain and its relation to structure formation. Two mutants, K28C/H124C and K28C/K97C, were constructed and labeled for monitoring the behaviors of the global molecule and the beta subdomain, respectively. For both the labeled mutants, only native and non-native conformations were observed, and the non-native conformations expanded with increasing GdmCl concentrations. The non-native chains of the two derivatives exhibited different changes of persistence length at higher GdmCl concentrations, suggesting a subdomain-specific collapse of the denatured state of SNase. This local chain specific collapse is likely to play a role in modulating the formation of early intermediate during protein folding.