Evolutionary geneticists currently face a major scientific opportunity when integrating across the rapidly increasing amount of genetic data and existing biological scenarios based on ecology, fossils or climate models. Although genetic data acquisition and analysis have improved tremendously, several limitations remain. Here, we discuss the feedback between history and genetic variation in the face of environmental change with increasing taxonomic and temporal scale, as well as the major challenges that lie ahead. In particular, we focus on recent developments in two promising genetic methods, those of ‘phylochronology’ and ‘molecular clocks’. With the advent of ancient DNA techniques, we can now directly sample the recent past. We illustrate this amazing and largely untapped utility of ancient DNA extracted from accurately dated localities with documented environmental changes. Innovative statistical analyses of these genetic data expose the direct effect of recent environmental change on genetic endurance, or maintenance of genetic variation. The ‘molecular clock’ (assumption of a linear relationship between genetic distance and evolutionary time) has been used extensively in phylogenetic studies to infer time and correlation between lineage divergence time and concurrent environmental change. Several studies at both population and species scale support a persuasive relationship between particular perturbation events and time of biotic divergence. However, we are still a way from gleaning an overall pattern to this relationship, which is a prerequisite to ultimately understanding the mechanisms by which past environments have shaped the evolutionary trajectory. Current obstacles include as–yet undecided reasons behind the frequent discrepancy between molecular and fossil time estimates, and the frequent lack of consideration of extensive confidence intervals around time estimates. We suggest that use and interpretation of both ancient DNA and molecular clocks is most effective when results are synthesized with palaeontological (fossil) and ecological (life history) information.