Charophyte assemblages from the Cretaceous/Paleogene (K/Pg) boundary transition in the JZK-2 borehole of the Jiaolai Basin (eastern China) were studied. The charophyte flora includes Tolypella grambastii, Peckichara praecursoria, Microchara cristata, Microchara prolixa, Chara changzhouensis, Lamprothamnium ellipticum, Nodosochara (Turbochara) specialis, Lychnothamnus aff. vectensis, and Lychnothamnus lanpingensis n. comb. The discovery of the ostracod species Porpocypris sphaeroidalis Guan in the upper section of the JZK-2 borehole strongly indicates the arrival of the Paleocene. Three floras of the latest Cretaceous to the early Paleocene were compared among the Jiaolai, Pingyi, and Songliao basins. The Pingyi Basin is special because it is the only carbonate palaeolake that occurred throughout the K/Pg transition in China. It is characterized by the appearance of the Cretaceous brackish water element, Feistiella anluensis (Wang), and is dominated by the Paleocene species, Peckichara varians Grambast. The Songliao and Jiaolai floras grow in clastic lakes; the Jiaolai Basin is thought to correspond to an altitude lake, which was formed in the coastal mountains with high palaeoelevation (≥ 2.0 km), while the Songliao Basin is presumed to have been formed in a low elevation site according to previous studies. This difference in altitude explains why the Songliao Basin is more species-rich than the Jiaolai Basin.