In this study, we investigated the genetic structure and phylogeographic pa
ttern of the genus Cunninghamia, a member of the Cupressaceae restricted to
mainland China and Taiwan, based on sequences of the trnD-trnT noncoding s
pacer of the chloroplast DNA. Maternal inheritance of chloroplasts was dete
rmined experimentally. No paternal leakage was detected. Both parsimony and
neighbor-joining analyses revealed the polyphyly of Cunninghamia konishii,
populations of which were nested in clades of C. lanceolata from mainland
China. The nucleotide diversity of chloroplast DNA sequences within C. koni
shii (0.0118) was higher than that between species (0.0104), which agrees w
ith a previous allozyme investigation. Based on mutational differences betw
een sequences, a minimum spanning network consisting of five clades was con
structed. Significant genetic differentiation (Phi (ST) = 0.130, P < 0.001)
was detected between the clades based on AMOVA analyses. We infer several
possible refugia in the Yunnan, Zhejiang, and Guangdong provinces of south
China, all located in the minimum network as interior nodes. We also infer
possible migration routes of Cunninghamia populations. The phylogeographic
pattern shown in the reconstructed network suggests that the present-day Cu
nninghamia populations in Taiwan were derived from six different sources in
continental Asia via long-distance seed dispersal. A migrant-pool model ex
plains the heterogeneous composition of the organelle DNA in Taiwan's popul
ations and the low differentiation between populations of Taiwan and China
(<Phi>(CT) = 0.012, P = 0.454). In contrast with the genetic heterogeneity
within geographic populations, many local populations have attained coalesc
ence at the trnD-trnT alleles, which has led to significant differentiation
at the population level.