He was previously a postdoctoral fellow at the National Institute for Mathematical and Biological Synthesis. Matzke is currently a phylogeneticist at the School of Biological Scienes at the University of Auckland, having previously been a Discovery Early Career Research Award (DECRA) fellow at the Australian National University.
Prior to his current position as a phylogeneticist at the University of Auckland's School of Biological Sciences, Matzke held a postdoctoral fellowship at the National Institute for Mathematical and Biological Synthesis. He was also a DECRA fellow at the Australian National University.