The main purpose of this paper is the extension of the classical spectral direct and inverse analysis of Jacobi matrices for the non-self-adjoint setting. Matrices of this class appear in the context of non-Hermitian quantum mechanics. The reconstruction of a pseudo-Jacobi matrix from its spectrum and the spectra of two complementary principal matrices is investigated in the context of indefinite inner product spaces. An existence and uniqueness theorem is given, and a strikingly simple algorithm, based on the Euclidean division algorithm, to reconstruct the matrix from the spectral data is presented. A result of Friedland and Melkman stating a necessary and sufficient condition for a real sequence to be the spectrum of a non-negative Jacobi matrix is revisited and generalized. Namely, it is shown that a suitable set of prescribed eigenvalues defines a unique non-negative pseudo-Jacobi matrix, which is J-Hermitian for a fixed J. Copyright © 2012 John Wiley & Sons, Ltd.