Abstract   The molecular clock hypothesis is a central concept in molecular evolution and has inspired much research into why evolutionary rates vary between and within genomes. In the age of modern comparative genomics, understanding the neutral genomic molecular clock occupies a critical place. It has been demonstrated that molecular clocks run differently between closely related species, and generation time is an important determinant of lineage specific molecular clocks. Moreover, it has been repeatedly shown that regional molecular clocks vary even within a genome, which should be taken into account when measuring evolutionary constraint of specific genomic regions. With the availability of a large amount of genomic sequence data, new insights into the patterns and causes of variation in molecular clocks are emerging. In particular, factors such as nucleotide composition, molecular origins of mutations, weak selection and recombination rates are important determinants of neutral genomic molecular clocks.