We localized the BoNT regions that bind blocking Abs from 28 BoNT/A- and 30 BoNT/B-treated dystonia patients who became unresponsive to correlate toxin. The sera protected mice against LD100 of correlate BoNT. We analyzed Ab binding to BoNT/A- and BoNT/B-H-chain peptide panels, each being 60, 19-residue peptides overlapping by 5 residues and covering the entire correlate H chain. Abs bound to a limited set of peptides but levels varied with patient, consistent with responses to each epitope being under separate MHC control. BoNT/B-treated patients had higher anti-toxin Ab levels and bound more H regions (at least 11) than BoNT/A-treated patients (5 regions). The epitopes were on surface areas that did not correlate with surface electrostatic potential, hydrophilicity, hydrophobicity, or temperature factor. Some epitopes within the two toxins display substantial homology and occupy analogous 3-D locations, occasionally showing a small shift relative to one another, consistent with recognition adjustments due to structural differences between the two BoNTs. Blocking Abs bound to BoNT/A at sites that coincide or overlap with synaptosome-binding, thus preventing its binding and blocking its entry into the neuron. On BoNT/B, a mouse-Ab binding region overlapped with a site that binds to mouse and rat synaptotagmin II, thus explaining Abs blocking action.