Especially DNA, RNA, or polypeptide sequences that are .

In genomes these similarities can be seen in orthologous genes, paralogous genes, or instead as a consequence of horizontal gene transfer. Often similarities persist longer over in polypeptide sequences or, indeed, polypeptide structure, than in genome sequence.

Molecular homologies can also be seen in organism physiologies, though physiological similarities can be more likely to exist as homoplasies (analogous similarities) rather than as homologies. The more complicated as well as similar in many aspects two physiologies, however, the more like that they are similar due to (though not necessarily due solely to ).

Contrast with morphological homologies.