To have a better understanding of the genetic diversity of Houttuynia cordata at the cytological level, the chromosome number and meiosis of pollen mother cells of 90 accessions from China were observed. The species exhibits highly complex variation in chromosome number, with the number varying from 36 to 126, of which 36, 54, 72 and 126 are reported for the first time and the number 81 is the most frequent one. The basic number of this species, the only member of the monotypic genus Houttuynia, might be considered to be 9. Cytomixis was observed for the first time in the species during the diad, tetrad and microspore periods. The chromatin was found to transfer through plasmodesma, conjugation opening and conjugation tube.