Chloroplast DNA (cpDNA) atpB-rbcL intergenic spacers of individuals of Alsophila podophylla, collected from eight relict populations distributed in Hainan and Guangdong Province, southern China, were sequenced. Sequence sizes were 726 or 727bp. Base composition had a high A T content of 62.67–63.00%. Sequences were assessed as evolutionarily neutral (Tajima's criterion D = −0.80683, P > 0.10 and Fu and Li's test D* = 1.42648, P > 0.05; F* = 0.76638, P > 0.10). Eight haplotypes were identified based on a statistical parsimony algorithm. A high level of haplotype diversity (h = 0.618) and a low nucleotide diversity (Dij = 0.00208) were detected in A. podophylla. Populations from Hainan shared common haplotypes with those from Guangdong. A network and a NJ tree constructed from cpDNA haplotypes both suggested a close genetic relationship among populations distributed in Hainan and Guangdong. Observed FST (=0.10537), gene flow Nm (=2.12), AMOVA (Only 0.49% of variation was partitioned among regions, P = 0.09), and DNA divergence data consistently indicated that no geographical differentiation occured at the interregional level. Geographic isolation has not yet resulted in population differentiations within A. podophylla populations in Hainan and Guangdong. Phylogeographical patterns of atpB-rbcL haplotypes demonstrate a ‘star-like’ feature, which means that populations of A. podophylla have experienced population expansion, and, since then there has been insufficient time to form a more complicated population structure. The majority of haplotypes coalesced near the tip of the NJ tree, indicating recent coalescence events as well. Moreover, a demographic signature of population expansion was detected by mismatch distribution analysis of atpB-rbcL sequences of A. podophylla.