The Pingtan and Tonglu igneous complexes in SE China are typical of the calc-alkaline series developed at active continental margins. These two complexes are dominated by felsic rocks, temporally and spatially associated with minor mafic rocks. Morphological and trace-element studies of zircon populations in rocks from each of these complexes show that the zircon populations may be divided into 3–4 distinct growth stages, characterized by different distributions of morphological indices (Ipr, Ipy and Iel), and different contents of the substituting elements (Hf, U, Th, Y and P). The four growth stages recognized in the zircons are believed to have formed successively in the magma chamber, during the emplacement, and in the early and later stages of magma consolidation, respectively. All four stages are recognized in the plutonic Pingtan complex, whereas the stages 3 and 4 are less developed in the volcanic/subvolcanic Tonglu complex. Based on the chemistry and morphology of the different zircon populations of the Pingtan and Tonglu complexes, it is suggested that basaltic magmas underplating at the boundary between crust and mantle caused partial melting of the mid–lower crust and produced granitoid magmas. Subsequently, mixing between magmas was important.