We study isogenies between K3 surfaces in positive characteristic. Our main result is a characterization of K3 surfaces isogenous to a given K3 surface $X$ in terms of certain integral sublattices of the second rational $ell$-adic and crystalline cohomology groups of $X$. This is a positive characteristic analog of a result of Huybrechts, and extends results of the second author. We give applications to the reduction types of K3 surfaces and to the surjectivity of the period morphism. To prove these results we describe a theory of B-fields and Mukai lattices in positive characteristic, which may be of independent interest. We also prove some results on lifting twisted Fourier--Mukai equivalences to characteristic 0, generalizing results of Lieblich and Olsson.
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