Temporal information on mammalian evolution allows testing of hypotheses about the mode of speciation and extinction, comparison of rates of evolution across taxa, and correlation of cladogenesis with important geological processes. Important insights can be made from combining data from fossils and molecules (DNA sequences), and relevant methods are expanding. When considering these methods, careful consideration should be given to features affecting time estimation (e.g., accuracy of tree construction, branch length estimation, taxonomic and genomic sampling, and sources of genetic and calibration errors). We report on the available methods that aid in evolutionary time estimation from molecular data and corresponding fossils. We recommend several steps to improve this process. First, we recommend using appropriate DNA substitution models to help correct DNA distance estimates and construct trees with more reliable branch lengths. Second, we recommend using multiple fossil calibration dates where possible. Third, in general, we recommend a conservative approach to time estimation by reporting inherent errors associated with genetic distances, calibration selection and application. In conclusion, temporal data derived from molecular clocks should be regarded in light of their dependence on paleontological information and their synergy with fossil data rather than competing with paleontological information. Thus, despite the varied sources of error, we encourage the extraction of time from molecular data with careful examination of potential biases.