Acid sensing ion channels (ASICs) are neuronal cation selective channels that respond to sudden drops in extracellular pH and desensitize in the continuous presence of protons. The mechanism that allows these channels to sense and respond to changes in extracellular pH is not well understood. Here we examined the contribution to channel activation of the finger and thumb domains of ASIC1a, two areas that reside in close proximity in the periphery of the extracellular region. Residues located at the interface of these two domains were individually mutated to Cys and the reactivity of the mutant channels toward the thiol reactive reagent MTSET was assessed using the two-electrode voltage clamp technique. We identified seven sites in the thumb domain, positions 325, 327, 344, 345, 348, 351 and 352, and two in the finger domain, positions 152 and 154, where MTSET treatment reduced the magnitude of the response to extracellular acidification. Residues 325, 327, 344, 345, 348 in the thumb domain are oriented toward residues 152 and 154 in the finger domain in the solved atomic structure of ASIC1 at low pH. Our results indicate that the finger and thumb domains experience a conformational change and become closer in response to extracellular acidification. To further assess the role of the finger-thumb interactions in ASIC1a proton activation, we generated channels with substitutions at neighboring positions in the finger and thumb domains. We found that the response to extracellular acidification after MTSET treatment of double mutant channels bearing Cys substitutions at positions 154 and 325 was significantly lower than the response of channels bearing individual mutations at these positions, consistent with functional coupling between the finger and thumb domain. Taken together, our results suggest that the finger and thumb domains contribute to ASIC1a activation.