Estimations of based on of nucleotide sequences that is thought to occur at more or less constant rates.
Molecular clocks are based predominantly on rates of fixation of neutral, that is, non- (not beneficial) alleles. These alleles are thought to enter populations and rise to fixation at a more or less constant though nonetheless relatively low rates.
In comparing the equivalent nucleotide sequences (orthologous genes), the degree of divergence can provide information as to how far back the common ancestor to the two species and therefore two genes can be found.
Note that molecular clocks at best provide the relative age of points of divergence, though can be converted to more absolute measures based particularly on evidence gleaned from the fossil record.