The genus Parrotia C. A. Mey. (Hamamelidaceae) contains just two extant deciduous broad-leaved trees, namely Parrotia subaequalis (H. T. Chang) R. M. Hao & H. T. Wei and P. persica (DC.) C. A. Mey. P. subaequalis, classified as a ‘Grade Ⅰ Key Protected Wild Plant’, is native to eastern China and belongs to East Asian Tertiary relics. Its sibling species, P. persica, is a member of the Arcto-Tertiary relict plant group and is disjunctly distributed in northern Iran. In this study, we estimated for the first time the genome size of the two species of Parrotia using flow cytometry and k-mer analysis, and established and optimized a suitable system for flow cytometric determination of DNA C value of these two plants, selecting Raphanus sativus L. ‘Saxa’ as the internal standard and WPB (woody plant buffer) as the nuclear dissociation solution. Our present research aims to provide a fundamental guidance for whole genome sequencing, genomics research, germplasm resource development and utilization, and species conservation of Parrotia and set an important example for the estimation of the genome size of other genera and species of the Hamamelidaceae. The main findings are as follows: (1) measurement results of the flow cytometry showed that the estimated genome size of P. subaequalis and P. persica was 971.45 ± 13.91 Mb and 890.52 ± 24.69 Mb, respectively; (2) k-mer analysis estimated that the genome size of P. subaequalis was about 951.70 Mb, the hybridity rate was about 1.740%, and the proportion of repeated sequences was about 77.50%; while for P. persica, the genome size, hybridity rate and the percentage of repeated sequences were 858.50 Mb, 0.695% and 74.30%, respectively; (3) the genome of P. subaequalis is classified as a highly heterozygous and highly repeated genome, while the genome of P. persica is a slightly heterozygous and highly repeated genome. Accordingly, the results of this study provide an important database reference for the follow-up work of whole-genome sequencing, assembly and de-redundancy processing of Parrotia based on DNA third-generation high-throughput sequencing technology.