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The genus Chamaecyparis (Cupressaceae) is comprised of six taxa native to East Asia and North America. Two independent lineages from eastern North America to East Asia and from western North America to East Asia have been identified from phylogenetic analyses based on variation in plastid DNA (ptDNA). However, the trees inferred from a nuclear ribosomal internal transcribed spacer (nrITS), the NEEDLY intron 2, and combined data from genetic and morphological characters of other studies are incongruent with the tree inferred from ptDNA. In this study, we sequenced the plastid matK gene as well as other sequences acquired from GenBank including the matK, rbcL, and nrITS sequences to reconstruct the phylogenetic trees of Chamaecyparis. The phylogenetic topology inferred from matK was congruent with the previous inference obtained using other ptDNA markers while the rbcL and ITS trees were congruent with previously inferred trees using the combined data and ITS sequences, respectively. Relatively less- (rbcL) and more-informative sites (ITS) may lead to different lineage sorting and incongruent phylogenetic topologies, which were evidenced by rejection of evolutionary homogeneity between ptDNA and ITS sequences in the partition homogeneity test. The phylogenetic tree reconstructed using matK and other ptDNA strongly supports the geographically disjunct distribution of Chamaecyparis in North America and East Asia. A dispersal-vicariance analysis, and geologic and fossil evidence indicated that at least two independent dispersal events occurred from North America to East Asia, which support the previous biogeographic inference by ptDNA. The use of biparental inherited markers for biogeographic inferences should be done with caution. [ABSTRACT FROM AUTHOR]