Rotifer is a major group of zooplankton; studies on its phylogeographical pattern and population genetic structure can make substantial contributions to understanding the processes such as population differentiation,speciation, ecological adaptation and historical climate change. Up to now, two opposite results exist in the phylogeographical pattern of rotifer populations. Firstly, high levels of population genetic subdivision and pronounced phylogeographical structure in rotifers are revealed due to the rapid population growth and founding events. In the second contrasting scenario,due to high dispersal capacity and regional adaptation,no phylogeographical structure is found. Seasonal variation in genetic structure may also bias our understanding of the observed phylogeographical pattern of rotifer populations. In this paper,we summarized the research progress on the phylogeographical pattern and population genetic structure of rotifer and gave a perspective on this field.