Geoemydidae is the largest and most diverse family in the order Testudines. The early study on phylogeny of Geoemydidae was conducted based on morphological and cytological features. In recent years, with the increasing molecular data and advanced morphology methods, the studies on phylogeny of Geoemydidae have been developed in many aspects, but its phylogenetic relationship is still uncertain. This review describes the origin of monophyly of the Geoemydidae; the most recent reassignment of the genus Batagur, Cuora and Mauremy; the intergeneric relationships among the genus Batagur, Pangshura, and Hardella, as well as Cyclemys, Heosemys, and Notochelys; the interspecific relationships in the genus Cyclemys and Rhinoclemmys, in order to offer references in phylogeny and conservation biology research of Geoemydidae.