Geological events and dramatical global climate changes over the Cenozoic, in particular Quaternary climatic oscillations, have remarkable influences on most temperate flora in their distribution, population structure and speciation. With the development of molecular markers and analysis methods in recent years, a lot of work in plant phylogeography has been done for studying response to changes of geology and climate and historical causes of population genetic differentiation by using phylogeny and distribution of time and space of genes. However, a few problems have been neglected in these excellent studies of plant phylogeography. In this paper, we try to sort these problems out by focusing on analysis methods and common softwares and to speculate the directions of future development.