Molecular clocks are the basis for dating the divergence between lineages over macroevolutionary timescales (~10 5 to 10 8 years). However, classical DNA-based clocks tick too slowly to inform us about the recent past. Here, we demonstrate that stochastic DNA methylation changes at a subset of cytosines in plant genomes display a clocklike behavior. This “epimutation clock” is orders of magnitude faster than DNA-based clocks and enables phylogenetic explorations on a scale of years to centuries. We show experimentally that epimutation clocks recapitulate known topologies and branching times of intraspecies phylogenetic trees in the self-fertilizing plant Arabidopsis thaliana and the clonal seagrass Zostera marina , which represent two major modes of plant reproduction. This discovery will open new possibilities for high-resolution temporal studies of plant biodiversity. Editor’s summary Molecular clocks provide the basis for many population genetic and evolutionary inferences, but are limited in use for recent generations because of low germline mutation rates. In plants, heritable changes in epigenetic markers, known as epimutations, occur at higher rates than genetic mutations. Yao et al . were able to develop a tool that allows for the estimation of phylogenies based on these epimutations (see the Perspective by Satyaki). The authors located regions of the genome that experience neutral, clock-like epimutations in the classic plant model Arabidopsis thaliana and were able to recapitulate known phylogenies of very recent time scales. This study will help to provide the tools and theoretical basis for estimating recent phylogenies in many plant species. —Corinne Simonti A fast-ticking evolutionary epigenetic clock in plants facilitates phylogenetic insights into the recent past.