Genetic code involving inherited DNA present as a single copy, which for eukaroyotes is the mitochondrion and in bacteria is the complete genome.

A haplotype most accurately describes the genetic code of the mitochondrion or a bacterial genome. Mutational changes in the mitochondrion haplotype can only have occurred as a result of point mutation. In bacterial haplotypic change can involve recombination. Haplotypic data albeit often limited in its genetic variation is considered robust because there is no ambiguity in base calling, unless for bacteria there is a mixed infection.