Plastid genomes have become an important source of information for clarifying phylogenetic relationships especially where traditional molecular systematic studies have failed to produce strongly supported hypotheses. The exact phylogenetic position of an early diverging fern order Hymenophyllales has remained uncertain due to poor support in published phylogenetic studies. High-throughput sequencing of the first complete plastid genome of the genus Trichomanesrevealed genome structure similar to the closest relatives and the phylogenetic analysis resulted in equally poorly supported topology as the previous studies that were based on only a few molecular markers. It seems that, at least with the current poor taxonomic sampling of complete plastid genomes, the exact relationships between Hymenophyllales, Gleicheniales, and other nonosmundalean leptosporangiate ferns cannot be firmly established.