Abstract Summary: Relaxed molecular clocks allow the phylogenetic estimation of evolutionary timescales even when substitution rates vary among branches. In analyses of large multigene datasets, it is often appropriate to use multiple relaxed-clock models to accommodate differing patterns of rate variation among genes. We present ClockstaR, a method for selecting the number of relaxed clocks for multigene datasets. Availability: ClockstaR is freely available for download at http://sydney.edu.au/science/biology/meep/software/. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.