A nilmanifold is a (left) quotient of a nilpotent Lie group by a cocompact lattice. A hypercomplex structure on a manifold is a triple of complex structure operators satisfying the quaternionic relations. A hypercomplex nilmanifold is a compact quotient of a nilpotent Lie group equipped with a left-invariant hypercomplex structure. Such a manifold admits a whole 2-dimensional sphere $S^2$ of complex structures induced by quaternions. We prove that for any hypercomplex nilmanifold $M$ and a generic complex structure $Lin S^2$, the complex manifold $(M,L)$ has algebraic dimension 0. A stronger result is proven when the hypercomplex nilmanifold is abelian. Consider the Lie algebra of left-invariant vector fields of Hodge type (1,0) on the corresponding nilpotent Lie group with respect to some complex structure $Iin S^2$. A hypercomplex nilmanifold is called abelian when this Lie algebra is abelian. We prove that all complex subvarieties of $(M,L)$ for generic $Lin S^2$ on a hypercomplex abelian nilmanifold are also hypercomplex nilmanifolds.
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