We study the isotropic Quot schemes parameterizing degree isotropic subsheaves of maximal rank of an orthogonal bundle over a curve. The scheme contains a compactification of the space of degree maximal isotropic subbundles, but behaves quite differently from the classical Quot scheme, and the Lagrangian Quot scheme in [6]. We observe that for certain topological types of , the scheme is empty for all . In the remaining cases, for infinitely many there are irreducible components of consisting entirely of nonsaturated subsheaves, and so is strictly larger than the closure of . As our main result, we prove that for any orthogonal bundle and for , the closure of is either empty or consists of one or two irreducible connected components, depending on and . In so doing, we also characterize the nonsaturated part of when has even rank.

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