We generalize Mukai and Shafarevich's definition of isogenies between K3 surfaces over C to an arbitrary perfect field and describe how to construct isogenous K3 surfaces over Fp by prescribing linear algebraic data when p is large. The main step is to show that isogenies between Kuga-Satake abelian varieties induce isogenies between K3 surfaces, in the context of integral models of Shimura varieties. As a byproduct, we show that every K3 surface of finite height admits a CM lifting under a mild assumption on p.Surjectivity of the period map gives us a complex analytic K3 X ′ which corresponds to the induced Hodge structure on Λ. Then one can use [3, IV Theorem 6.2] to see that X ′ has to be algebraic.We give an analogue of Theorem 1.2 for quasi-polarized K3 surfaces over Fp , using K3 crystals and Z p -lattices to replace Z-lattices. K3 crystals were originally defined by Ogus to characterize the F-crystals that arise from K3 surfaces (c.f. [34, Definition 3.1]): Definition 1.3. Let k be a perfect field of characteristic p > 0 and let σ be the lift of Frobenius on W (k). A K3 crystal over k is a finitely generated free W (k)-module D equipped with a σ-linear injection ϕ : D → D and a perfect symmetric bilinear pairing −, − such that ϕ(x), ϕ(y) = p 2 σ( x, y ), p 2 D ⊂ ϕ(D), and rank ϕ⊗k = 1.Recall that a quasi-polarized K3 surface is a pair (X, ξ) where X is a K3 surface and ξ is a primitive big and nef line bundle on X. We call the self-intersection number of ξ the degree of (X, ξ). Customarily, we write P 2 * (X) := ch * (ξ) ⊥ ⊂ H 2 * (X) for the primitive cohomology of (X, ξ) ( * = dR, cris, ét, etc). Our main theorem states: