Previous work with N-ethylmaleimide (NEM) has defined two sites on the Neurospora plasma membrane H+-ATPase. Modification of one (the "fast" site) by NEM is rapid but does not affect ATPase activity, while modification of the other (the "slow" site) inactivates the enzyme and is protectable by MgATP or MgADP. In the present study, a wider array of sulfhydryl reagents have been used to examine the properties of both sites. The results show the following. (a) Both fast and slow sites react preferentially with hydrophobic compounds (N-pyrenemaleimide, dithiobisnitropyridine greater than N-naphthylmaleimide, dithiobisnitrobenzoate greater than N-phenylmaleimide greater than N-ethylmaleimide) and are virtually insensitive to hydrophilic sulfhydryl reagents such as iodoacetamide and iodoacetic acid. (b) The reaction rate of the slow site with NEM is approximately 2000-fold less rapid than that of the fast site. The slow site also has an unusually high pKa (greater than 9.5). (c) Whether or not cysteine modification leads to inactivation of the ATPase depends upon the site and the reagent. For example, when the fast site reacts with NEM, enzymatic activity is retained; when it reacts with N-pyrenemaleimide, activity is lost. Likewise, when the slow site is modified by any of the maleimides or by dithiobisnitropyridine or dithiobisnitrobenzoate, the ATPase is inactivated; when it is modified by methylmethanethiosulfonate, activity remains intact. Thus, neither cysteine can be considered to play an essential role in the reaction cycle of the ATPase, but the introduction of a sufficiently bulky substituent at either site can disrupt activity. (d) Upon reaction of methylmethanethiosulfonate at the slow site, the K1/2 for MgATP hydrolysis is reduced from 0.65 to 0.25 mM. This result strengthens the evidence for a conformational relationship between the slow site cysteine and the nucleotide binding site of the ATPase.