There is provided a method of nucleic acid analysis which allows analysis of genetic diversity in multiple populations to be performed rapidly and simultaneously. The method comprises (a) isolating nucleic acid from said sample; (b) providing at least two pairs of labelled primers, wherein each said primer pair is complementary to a marker sequence in a nucleic acid of at least one member; (c) amplifying the nucleic acid; (d) digesting the labelled amplified nucleic acid with at least one restriction enzyme to produce restriction fragments, and size sorting said fragments to produce a restriction fragment length profile, and (e) analysing said restriction fragment length profile so obtained; wherein the primer pairs provided for each marker have a different sequence to the sequence of the primer pairs for each other marker, and wherein each said primer pair is uniquely labelled relative to the other primer pair(s). In one embodiment each primer pair is uniquely labelled at the 5′ end with a fluorophore. The restriction fragments can be conveniently analysed by a DNA sequencer. The method of the invention has the advantage that it allows nucleic acid amplified using multiple marker sequences to be simultaneously analysed.