The introns of chloroplast trnKUUU belong to Group II introns and contain an open reading frame denoted as matK. The trnK5’-matK-trnK3’ structure is consistent in almost all examined higher land plants and in Characeae, but not in other green algae examined. The putative gene product MatK is the only maturase in chloroplasts. Functional chloroplast matK genes are retained even in the nonphotosynthetic parasite, Epifagus virginiana and the fern, Adiantum capillus-veneris, in which chloroplast genome rearrangement has left matK free-standing, apart from trnK exons. Among lower land plants, the chloroplasts of Psilotum, mosses and liverworts all have trnK5’-matK-trnK3’ structure, but matK is a pseudogene in hornwort Anthoceros formosae. In this study we found a clear trnK5’-matK-trnK3’ structure in Ophioglossum petiolatum, Lycopodiella cernua and Selaginella doederleinii, but PCR with degenerate primers failed to amplify any trnK or matK fragments from other ferns and fern allies. However, dot blot hybridization showed distinct signals in these plants that failed to amplify matK fragments by PCR, indicating that the matK sequences in those taxa may be too divergent to amplify by an ordinary PCR approach. RT-PCR results showed matK genes are expressed in Ophioglossum petiolatum and Lycopodiella cernua, but no signal was detected in Selaginella doederleinii. Overall, the expression patterns of matK are not consistent in lower land plants. Phylogenetic analysis of matK sequence showed that Pinus, Ginkgo, and Cycas form a monophyletic group, which is sister to angiosperms. Together, they form a clade that is sister to Gnetales. This ad hoc reconstruction is likely due to the high evolutionary rate in matK.