In mathematics, a distance matrix is a matrix (two-dimensional array) containing the distances, taken pairwise, of a set of points. It is therefore a symmetric N×N matrix containing non-negative reals as elements, given N points in Euclidean space.

In bioinformatics, distances matrices are used to represent protein structures in a coordinate-independent manner, as well as the pairwise distances between two sequences in sequence space. They are used in structural and sequential alignment, and for the determination of protein structures from NMR or X-ray crystallography.

Sometimes it is more convenient to express data as a similarity matrix.